Gene	SNP Identifiers	SNP location	Genomic loci	Disease or Protective allele	Allele Frequency (GnomAD)	Literatures
ABCB1	rs1045642	Exon	7q21.12	Disease	> 0.01	Association between ABCB1, ABCG2 carrier protein and COX-2 enzyme gene polymorphisms and breast cancer risk in a Turkish population
ABCG2	rs2231142	Exon	4q22.1	Protective	> 0.01	Association between ABCB1, ABCG2 carrier protein and COX-2 enzyme gene polymorphisms and breast cancer risk in a Turkish population
ABHD8	rs10424198	Intron	19p13.11	Disease	> 0.01	Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
ABHD8	rs4808616	3 Prime UTR Variant	19p13.11	Disease	> 0.01	Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
ABR	-	CNV	17p13.3	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
ABRAXAS1	-	-	4q21.23	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
ABRAXAS1	rs11099601	3 Prime UTR Variant	4q21.23	Disease	> 0.01	Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21
ABRAXAS1	rs201627097	Exon	4q21.23	Disease	< 0.01	Breast Cancer-Associated Abraxas Mutation Disrupts Nuclear Localization and DNA Damage Response Functions
AC008132.1	-	CNV	22q11.21	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
AC058822.1	-	-	4q12	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
ACE	rs1799752	Intron	17q23.3	Disease	> 0.01	Association of AGTR1 (A1166C) and ACE (I/D) Polymorphisms with Breast Cancer Risk in North Indian Population
ACE	rs1799752	Intron	17q23.3	Disease	> 0.01	Genetic variation in angiotensin I-converting enzyme (ACE) and breast cancer risk: the multiethnic cohort
ACE	rs1799752	Intron	17q23.3	Disease	> 0.01	Association between the angiotensin-converting enzyme (insertion/deletion) and angiotensin II type 1 receptor (A1166C) polymorphisms and breast cancer among Brazilian women
ACOXL-AS1	rs73954922	Intron	2q13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ACOXL	rs73954922	Intron	2q13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ACTA2	rs1800682	Intron	10q23.31	Disease	> 0.01	Functional Polymorphisms of FAS and FASL Gene and Risk of Breast Cancer – Pilot Study of 134 Cases
ACTA2	rs2234767	Intron	10q23.31	Disease	> 0.01	Polymorphisms of the FAS and FASL genes and risk of breast cancer
ACYP2	rs12621038	Intron	2p16.2	Protective	> 0.01	Genetic variants in the acylphosphatase 2 gene and the risk of breast cancer in a Han Chinese population
ACYP2	rs1682111	Intron	2p16.2	Disease	> 0.01	Genetic variants in the acylphosphatase 2 gene and the risk of breast cancer in a Han Chinese population
ACYP2	rs17045754	Intron	2p16.2	Protective	> 0.01	Genetic variants in the acylphosphatase 2 gene and the risk of breast cancer in a Han Chinese population
ACYP2	rs843706	Intron	2p16.2	Disease	> 0.01	Association between single nucleotide polymorphisms in the TSPYL6 gene and breast cancer susceptibility in the Han Chinese population
ADAM29	rs6828523	Intron	4q34.1	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
ADAM29	rs6828523	Intron	4q34.1	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
ADARB2	rs74122632	Intron	10p15.3	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
ADCY3	rs6725517	Intron	2p23.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ADCY9	rs11076805	Intron	16p13.3	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
ADCY9	rs2601774	Intron	16p13.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ADSS1	rs10623258	Intron	14q32.33	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
AFDN	rs3778663	Intron	6q27	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AGTR1	rs5186	3 Prime UTR Variant	3q24	Disease	> 0.01	Association of AGTR1 (A1166C) and ACE (I/D) Polymorphisms with Breast Cancer Risk in North Indian Population
AHR	rs2066853	Exon	7p21.1	Disease	> 0.01	Genetic polymorphisms of estrogen metabolizing enzyme and breast cancer risk in Thai women
AHRR	rs62641919	Intron	5p15.33	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
AHRR	rs62641919	Intron	5p15.33	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AIRE	rs2075876	Intron	21q22.3	Protective	> 0.01	Analysis of the autoimmune regulator (AIRE) gene variant rs2075876 (G/A) association with breast cancer susceptibility
AKAP6	rs3784179	Intron	14q13.1	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
AKAP9	rs6960867	Exon	7q21.2	Disease	> 0.01	Association of a Common AKAP9 Variant With Breast Cancer Risk: A Collaborative Analysis
AKAP9	rs6964587	Exon	7q21.2	Disease	> 0.01	Association of a Common AKAP9 Variant With Breast Cancer Risk: A Collaborative Analysis
AKAP9	rs6964587	Exon	7q21.2	Disease	> 0.01	Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium
AKAP9	rs141039834	Exon	7q21.2	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
AKAP9	rs2075881	Intron	7q21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AKR1A1	rs35349030	Intron	1p34.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AKR1A1	rs3790585	Intron	1p34.1	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
AKT1	rs1130233	Exon	14q32.33	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
ALDH2	rs671	Exon	12q24.12	Disease	> 0.01	The functional ALDH2 polymorphism is associated with breast cancer risk: A pooled analysis from the Breast Cancer Association Consortium
ALG9	rs11354045	Intron	11q23.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ALOX12	rs1126667	Exon	17p13.1	Disease	> 0.01	Association of a functional polymorphism (Gln261Arg) in 12-lipoxygenase with breast cancer
ALOX12	rs434473	Exon	17p13.1	Disease	> 0.01	Associations between ALOX, COX, and CRP polymorphisms and breast cancer among Hispanic and non‐Hispanic white women: The breast cancer health disparities study
ALOX12	rs9904779	5 Prime UTR Variant	17p13.1	Disease	> 0.01	Associations between ALOX, COX, and CRP polymorphisms and breast cancer among Hispanic and non‐Hispanic white women: The breast cancer health disparities study
ALOX12-AS1	rs1126667	Intron	17p13.1	Disease	> 0.01	Association of a functional polymorphism (Gln261Arg) in 12-lipoxygenase with breast cancer
ALOX12-AS1	rs434473	Intron	17p13.1	Disease	> 0.01	Associations between ALOX, COX, and CRP polymorphisms and breast cancer among Hispanic and non‐Hispanic white women: The breast cancer health disparities study
ALOX12-AS1	rs9904779	Intron	17p13.1	Disease	> 0.01	Associations between ALOX, COX, and CRP polymorphisms and breast cancer among Hispanic and non‐Hispanic white women: The breast cancer health disparities study
AMFR	rs2432539	Intron	16q13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
AMFR	rs2432539	Intron	16q13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ANGPT2	rs1823375	Intron	8p23.1	Protective	> 0.01	The impact of Angiopoietin-2 genetic polymorphisms on susceptibility for malignant breast neoplasms
ANKLE1	rs56069439	Intron	19p13.11	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
ANTXR1	rs4602255	Intron	2p13.3	Disease	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
ANTXR1	rs62134416	Intron	2p13.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AP4B1-AS1	rs11102694	Intron	1p13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
APC	rs1801155	Exon	5q22.2	Disease	< 0.01	The APC I1307K allele conveys a significant increased risk for cancer
APC	rs454886	Intron	5q22.2	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
APEX1	rs1130409	Exon	14q11.2	Disease	> 0.01	Association of Polymorphisms in Base Excision Repair Genes With the Risk of Breast Cancer: A Case-Control Study in North Indian Women
APEX1	rs1130409	Exon	14q11.2	Disease	> 0.01	Association of DNA Repair Gene APE1 Asp148Glu Polymorphism With Breast Cancer Risk
APEX1	rs1130409	Exon	14q11.2	Protective	> 0.01	Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk
APOBEC3A	rs12628403	Intron	22q13.1	Disease	> 0.01	A Common Deletion in the APOBEC3 Genes and Breast Cancer Risk
APOBEC3A_B	rs12628403	Intron	22q13.1	Disease	> 0.01	A Common Deletion in the APOBEC3 Genes and Breast Cancer Risk
APOBEC3A_B	rs12628403	Intron	22q13.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
APOBEC3A	rs12628403	Intron	22q13.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AQP4-AS1	rs745983748	Intron	18q11.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ARHGAP26	rs13172733	Intron	5q31.3	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
ARHGAP26	rs153170	Intron	5q31.3	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
ARHGEF5	rs720475	Intron	7q35	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
ARL11	rs3803185	Exon	13q14.2	Disease	> 0.01	Association of the ARLTS1 Cys148Arg variant with familial breast cancer risk
ARLNC1	rs1981867	Intron	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
ASPH	rs2350923	Intron	8q12.3	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
ASPRV1	rs6756513	Intron	2p13.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ASTN2	rs1895062	Intron	9q33.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ASTN2-AS1	rs1407243	Intron	9q33.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ASTN2-AS1	rs1895062	Intron	9q33.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ASTN2	rs1407243	Intron	9q33.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ATAD5	rs7223535	Intron	17q11.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ATE1	rs10510102	Intron	10q26.13	Disease	> 0.01	Novel Breast Cancer Susceptibility Locus at 9q31.2: Results of a Genome-Wide Association Study
ATG10	rs10514231	Intron	5q14.2	Protective	> 0.01	Potentially functional polymorphisms in ATG10 are associated with risk of breast cancer in a Chinese population
ATG10	rs1864182	Exon	5q14.2	Protective	> 0.01	Potentially functional polymorphisms in ATG10 are associated with risk of breast cancer in a Chinese population
ATG10	rs7707921	Intron	5q14.2	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
ATG10	rs4081859	Intron	5q14.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ATM	-	CNV	11q22.3	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
ATM	-	Exon	11q22.3	Disease	< 0.01	Evaluation of the Role of Finnish Ataxia-Telangiectasia Mutations in Hereditary Predisposition to Breast Cancer
ATM	-	Exon	11q22.3	Disease	< 0.01	ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles
ATM	-	Exon	11q22.3	Disease	< 0.01	Cancer risks and mortality in heterozygous ATM mutation carriers
ATM	-	Exon	11q22.3	Disease	< 0.01	Breast cancer risk in ataxia telangiectasia (AT) heterozygotes: haplotype study in French AT families
ATM	-	Exon	11q22.3	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
ATM	-	Exon	11q22.3	Disease	< 0.01	Male breast cancer risk associated with pathogenic variants in genes other than BRCA1/2: an Italian case-control study
ATM	-	Exon	11q22.3	Disease	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
ATM	-	Exon	11q22.3	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
ATM	rs609429	Intron	11q22.3	Disease	> 0.01	ATM Haplotypes and Cellular Response to DNA Damage: Association with Breast Cancer Risk and Clinical Radiosensitivity
ATM	rs664677	Intron	11q22.3	Disease	> 0.01	ATM Haplotypes and Cellular Response to DNA Damage: Association with Breast Cancer Risk and Clinical Radiosensitivity
ATM	rs228590	Intron	11q22.3	Disease	> 0.01	SDC4-rs1981429 and ATM-rs228590 may provide early biomarkers of breast cancer risk
ATM	rs769142993	Exon	11q22.3	Disease	< 0.01	ATM c.7570G>C is a high-risk allele for breast cancer
ATP12A	-	CNV	13q12.12	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
ATR	rs2227931	Exon	3q23	Protective	> 0.01	Mutation analysis of the ATR gene in breast and ovarian cancer families
ATR	rs6805118	Intron	3q23	Protective	> 0.01	Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer
ATR	rs768843213	Intron	3q23	Disease	< 0.01	Mutation analysis of the ATR gene in breast and ovarian cancer families
ATRIP	rs753154444	Exon	3p21.31	Disease	< 0.01	Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank
ATXN1	rs3819405	Intron	6p22.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ATXN1	rs3819405	Intron	6p22.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ATXN7	rs1053338	Exon	3p14.1	Disease	> 0.01	Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium
ATXN7	rs73117066	Intron	3p14.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
AURKA	rs1047972	Exon	20q13.2	Protective	> 0.01	AURKA Gene Variants rs1047972, and rs8173 Are Associated With Breast Cancer
AURKA	rs8173	3 Prime UTR Variant	20q13.2	Protective/Disease	> 0.01	AURKA Gene Variants rs1047972, and rs8173 Are Associated With Breast Cancer
AXIN2	rs11079571	Intron	17q24.1	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
AXIN2	rs11079571	Intron	17q24.1	Disease	> 0.01	The Association Between AXIN2 Gene Polymorphisms and the Risk of Breast Cancer in Chinese Women
AXIN2	rs2240308	Exon	17q24.1	Disease	> 0.01	AXIN2 Polymorphisms, the β-Catenin Destruction Complex Expression Profile and Breast Cancer Susceptibility
AXIN2	rs2240308	Exon	17q24.1	Disease	> 0.01	Genotypes and Haplotypes in the AXIN2 and TCF7L2 Genes are Associated With Susceptibility and With Clinicopathological Characteristics in Breast Cancer Patients
AXIN2	rs3923086	Intron	17q24.1	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
AXIN2	rs3923086	Intron	17q24.1	Protective	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes With Breast Cancer in Saudi Patients
AXIN2	rs3923087	Intron	17q24.1	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
AXIN2	rs3923087	Intron	17q24.1	Protective	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes With Breast Cancer in Saudi Patients
AXIN2	rs3923087	Intron	17q24.1	Disease	> 0.01	The Association Between AXIN2 Gene Polymorphisms and the Risk of Breast Cancer in Chinese Women
AXIN2	rs4791171	Intron	17q24.1	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
AXIN2	rs7210356	Intron	17q24.1	Disease	> 0.01	Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer
BABAM1	rs8170	Exon	19p13.11	Disease	> 0.01	Genetic Susceptibility Loci for Subtypes of Breast Cancer in an African American Population
BABAM1	rs8170	Exon	19p13.11	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
BAIAP2L1	rs4439053	Intron	7q22.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
BAIAP2L1	rs79518236	Intron	7q21.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
BARD1	-	Exon	2q35	Disease	< 0.01	Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer
BARD1	-	Exon	2q35	Disease	< 0.01	Germline loss-of-function variants in the BARD1 gene are associated with early-onset familial breast cancer but not ovarian cancer
BARD1	-	Exon	2q35	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
BARD1	-	Exon	2q35	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
BARD1	rs28997576	Exon	2q35	Disease	> 0.01	The BARD1 Cys557Ser Variant and Risk of Familial Breast Cancer in a South-American Population
BARD1	rs28997576	Exon	2q35	Disease	> 0.01	Mutation screening of the BARD1 gene: evidence for involvement of the Cys557Ser allele in hereditary susceptibility to breast cancer
BARD1	rs28997576	Exon	2q35	Disease	> 0.01	Nordic Collaborative Study of the BARD1 Cys557Ser Allele in 3956 Patients With Cancer: Enrichment in Familial BRCA1/BRCA2 Mutation-Negative Breast Cancer but Not in Other Malignancies
BARD1	rs587780021	Exon	2q35	Disease	< 0.01	BARD1 is a Low/Moderate Breast Cancer Risk Gene: Evidence Based on an Association Study of the Central European p.Q564X Recurrent Mutation
BARD1	rs2229571	Exon	2q35	Protective	> 0.01	Mutations in exon region of BRCA1-related RING domain 1 gene and risk of breast cancer
BARD1	rs28997575	Exon	2q35	Disease	> 0.01	Mutations in exon region of BRCA1-related RING domain 1 gene and risk of breast cancer
BCKDHB	rs12207986	Intron	6q14.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
BCKDHB	rs1836962	Intron	6q14.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
BCL2L11	rs3833441	Non Coding Transcript Variant	2q13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
BCL2L15	rs11102694	Intron	1p13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
BET1	rs10953105	Intron	7q21.3	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
BIVM-ERCC5	rs17655	Exon	13q33.1	Disease	> 0.01	Synergistic Effects of Polymorphisms in DNA Repair Genes and Endogenous Estrogen Exposure on Female Breast Cancer Risk
BIVM-ERCC5	rs17655	Exon	13q33.1	Disease	> 0.01	The interplay between XPG-Asp1104His polymorphism and reproductive risk factors elevates risk of breast cancer in Tanzanian women: A multiple interaction analysis
BLM	rs200389141	Exon	15q26.1	Disease	< 0.01	High prevalence and breast cancer predisposing role of the BLM c.1642 C>T (Q548X) mutation in Russia
BLM	rs200389141	Exon	15q26.1	Disease	< 0.01	Nonsense mutation p.Q548X in BLM, the gene mutated in Bloom's syndrome, is associated with breast cancer in Slavic populations
BLM	rs2380165	Intron	15q26.1	Disease	> 0.01	Genetic variants of BLM interact with RAD51 to increase breast cancer susceptibility
BRCA1	-	CNV	17q21.31	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Breast and Ovarian Cancer Risks Due to Inherited Mutations in BRCA1 and BRCA2
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Genetic Heterogeneity and Penetrance Analysis of the BRCA1 and BRCA2 Genes in Breast Cancer Families
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Prevalence and penetrance of BRCA1 and BRCA2 gene mutations in unselected Ashkenazi Jewish women with breast cancer
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases
BRCA1	-	Exon	17q21.31	Disease	< 0.01	The Risk of Cancer Associated with Specific Mutations of BRCA1 and BRCA2 among Ashkenazi Jews
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Average Risks of Breast and Ovarian Cancer Associated with BRCA1 or BRCA2 Mutations Detected in Case Series Unselected for Family History: A Combined Analysis of 22 Studies
BRCA1	-	Exon	17q21.31	Disease	< 0.01	The Lifetime Risks of Breast Cancer in Ashkenazi Jewish Carriers of BRCA1 and BRCA2 Mutations
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies
BRCA1	-	Exon	17q21.31	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
BRCA1	-	Exon	17q21.31	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
BRCA1	-	Exon	17q21.31	Disease	-	Association between germline pathogenic variants and breast cancer risk in Japanese women: The HERPACC study
BRCA1	rs1799950	Exon	17q21.31	Disease	> 0.01	Significant association of BRCA1 (rs1799950), BRCA2 (rs144848) and TP53 (rs1042522) polymorphism with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan
BRCA2	-	CNV	13q13.1	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Breast and Ovarian Cancer Risks Due to Inherited Mutations in BRCA1 and BRCA2
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Genetic Heterogeneity and Penetrance Analysis of the BRCA1 and BRCA2 Genes in Breast Cancer Families
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Population-based study of risk of breast cancer in carriers of BRCA2 mutation
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Prevalence and penetrance of BRCA1 and BRCA2 gene mutations in unselected Ashkenazi Jewish women with breast cancer
BRCA2	-	Exon	13q13.1	Disease	< 0.01	The Risk of Cancer Associated with Specific Mutations of BRCA1 and BRCA2 among Ashkenazi Jews
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Average Risks of Breast and Ovarian Cancer Associated with BRCA1 or BRCA2 Mutations Detected in Case Series Unselected for Family History: A Combined Analysis of 22 Studies
BRCA2	-	Exon	13q13.1	Disease	< 0.01	The Lifetime Risks of Breast Cancer in Ashkenazi Jewish Carriers of BRCA1 and BRCA2 Mutations
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies
BRCA2	-	Exon	13q13.1	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
BRCA2	-	Exon	13q13.1	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
BRCA2	-	Exon	13q13.1	Disease	-	Association between germline pathogenic variants and breast cancer risk in Japanese women: The HERPACC study
BRCA2	rs11571833	Exon	13q13.1	Disease	< 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
BRCA2	rs144848	Exon	13q13.1	Disease	> 0.01	Significant association of BRCA1 (rs1799950), BRCA2 (rs144848) and TP53 (rs1042522) polymorphism with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan
BRCA2	rs11571833	Exon	13q13.1	Disease	< 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
BRD7	-	Exon	16q12.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
BRIP1	rs137852986	Exon	17q23.2	Disease	< 0.01	Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles
BTN2A1	-	-	6p22.2	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
C11orf65	rs609429	Intron	11q22.3	Disease	> 0.01	ATM Haplotypes and Cellular Response to DNA Damage
C11orf65	rs199504893	Intron	11q22.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
C11orf65	rs769142993	Non Coding Transcript Variant	11q22.3	Disease	< 0.01	ATM c.7570G>C is a high-risk allele for breast cancer
C2CD6	rs59278883	Intron	2q33.1	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
CABLES1	rs11082321	Intron	18q11.2	Disease	> 0.01	Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3, and 15q26.1
CASC15	rs7760611	Intron	6p22.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
CASC15	rs7765429	Intron	6p22.3	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
CASC15	rs7765429	Intron	6p22.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CASC16	rs12922061	Intron	16q12.1	Disease	> 0.01	The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population
CASC16	rs3803662	Non Coding Transcript Variant	16q12.1	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
CASC16	rs3803662	Non Coding Transcript Variant	16q12.1	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CASC16	rs3803662	Non Coding Transcript Variant	16q12.1	Disease	> 0.01	Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer
CASC16	rs3803662	Non Coding Transcript Variant	16q12.1	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
CASC16	rs4784227	Intron	16q12.1	Disease	> 0.01	Association of rs4784227-CASC16 (LOC643714 locus) and rs4782447-ACSF3 polymorphisms and their association with breast cancer risk among Iranian population
CASC16	rs4784227	Intron	16q12.1	Disease	> 0.01	The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population
CASC16	rs4784227	Intron	16q12.1	Disease	> 0.01	Fine scale mapping of the breast cancer 16q12 locus
CASC16	rs4784227	Intron	16q12.2	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
CASC16	rs4784227	Intron	16q12.2	Disease	> 0.01	Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population
CASC16	rs4784227	Intron	16q12.2	Disease	> 0.01	Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis
CASC16	rs3803662	Non Coding Transcript Variant	16q12.2	Protective	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
CASC16	rs4784227	Intron	16q12.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CASC16	rs4784227	Intron	16q12.2	Disease	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
CASC21	rs13281615	Intron	8q24.21	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
CASC21	rs13281615	Intron	8q24.21	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
CASC21	rs1562430	Intron	8q24.21	Protective	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
CASC21	rs1562430	Intron	8q24.21	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CASC21	rs10096351	Intron	8q24.21	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CASC8	rs13281615	Intron	8q24.21	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
CASC8	rs13281615	Intron	8q24.21	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
CASC8	rs1562430	Intron	8q24.21	Protective	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
CASC8	rs1562430	Intron	8q24.21	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CASC8	rs10096351	Intron	8q24.21	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CASP10	rs13010627	Exon	2q33.1	Protective	> 0.01	Association of the CASP10 V410I variant with reduced familial breast cancer risk and interaction with the CASP8 D302H variant
CASP8	rs1045485	Exon	2q33.1	Protective	> 0.01	A common coding variant in CASP8 is associated with breast cancer risk
CASP8	rs1045485	Exon	2q33.1	Protective	> 0.01	Commonly Studied Single-Nucleotide Polymorphisms and Breast Cancer: Results From the Breast Cancer Association Consortium
CASP8	rs10931936	Intron	2q33.1	Protective	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CASP8	rs10931936	Intron	2q33.1	Disease	> 0.01	Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran
CASP8	rs12990906	Intron	2q33.1	Disease	> 0.01	Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran
CASP8	rs3754934	Intron	2q33.1	Protective	> 0.01	Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran
CASP8	rs3834129	Intron	2q33.1	Disease	> 0.01	Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran
CASP8	rs7608692	Intron	2q33.1	Disease	> 0.01	Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran
CASP8	rs3769821	Intron	2q33.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CBFA2T3	rs61734177	Exon	16q24.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
CCDC152	rs3877899	3 Prime UTR Variant	5p12	Protective	> 0.01	Association between Polymorphisms in Glutathione Peroxidase and Selenoprotein P Genes, Glutathione Peroxidase Activity, HRT Use and Breast Cancer Risk
CCDC170	rs12662670	Intron	6q25.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
CCDC170	rs3757318	Intron	6q25.1	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CCDC170	rs3757322	3 Prime UTR Variant	6q25.1	Disease	> 0.01	Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
CCDC170	rs3757322	3 Prime UTR Variant	6q25.1	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
CCDC170	rs9383935	3 Prime UTR Variant	6q25.1	Disease	> 0.01	Evaluation of functional genetic variants at 6q25.1 and risk of breast cancer in a Chinese population
CCDC170	rs1038304	Intron	6q25.1	Protective	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
CCDC33	rs1484216	Intron	15q24.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CCDC88C	rs941764	Intron	14q32.11	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
CCDC88C	rs933986797	Intron	14q32.12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CCDC91	rs1871152	Intron	12p11.22	Disease	> 0.01	Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
CCND1	rs9344	Exon	11q13.3	Disease	> 0.01	Association of CCND1 (c.723G > A, rs9344) variant with elevated risk of breast carcinoma: a retrospective case-control study
CCNE1	rs1406	3 Prime UTR Variant	19q12	Disease	> 0.01	Association Between CCNE1 Polymorphisms and the Risk of Breast Cancer in a Sample of Southeast Iranian Population
CCNE1	rs997669	Intron	19q12	Disease	> 0.01	Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
CDC27	rs12601027	Intron	17q21.32	Disease	> 0.01	Association between polymorphisms in cdc27 and breast cancer in a Chinese population
CDCA7L	rs7971	3 Prime UTR Variant	7p15.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
CDCA7L	rs7971	3 Prime UTR Variant	7p15.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CDH1	-	Exon	16q22.1	Disease	< 0.01	Incidence of gastric cancer and breast cancer in CDH1 (E-cadherin) mutation carriers from hereditary diffuse gastric cancer families
CDH1	-	Exon	16q22.1	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
CDH1	rs3743674	Intron	16q22.1	Disease	> 0.01	Association of ATM, CDH1 and TP53 genes polymorphisms with familial breast cancer in patients of Khyber Pakhtunkhwa, Pakistan
CDK1	rs1871446	3 Prime UTR Variant	10q21.2	Protective	> 0.01	Association Study of Germline Variants in CCNB1 and CDK1 with Breast Cancer Susceptibility, Progression, and Survival among Chinese Han Women
CDK1	rs2448343	Intron	10q21.2	Protective	> 0.01	Association Study of Germline Variants in CCNB1 and CDK1 with Breast Cancer Susceptibility, Progression, and Survival among Chinese Han Women
CDKAL1	rs2223621	Intron	6p22.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
CDKAL1	rs1005745216	Intron	6p22.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CDKN1A	rs1801270	Exon	6p21.2	Disease	> 0.01	Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
CDKN1A	rs1801270	Exon	6p21.2	Protective	> 0.01	TP53 (rs1042522, rs28934571) and TP21 (rs1801270, rs1059234) Polymorphisms and Risk of Breast Cancer among Rural Women of Maharashtra: Findings from a Hospital Based Case- Control Study
CDKN1A	rs3829964	Intron	6p21.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CDKN1B	rs34330	5 Prime UTR Variant	12p13.1	Disease	> 0.01	Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
CDKN2A	rs3731249	Exon	9p21.3	Disease	> 0.01	A common variant of CDKN2A (p16) predisposes to breast cancer
CDKN2B-AS1	rs1011970	Intron	9p21.3	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
CDKN2B-AS1	rs1011970	Intron	9p21.3	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
CDYL2	rs13329835	Intron	16q23.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
CDYL2	rs12446424	Intron	16q23.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CEP131	rs9319617	Intron	17q25.3	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
CEP131	rs9896850	Intron	17q25.3	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
CEP131	rs9913021	Intron	17q25.3	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
CFAP20DC-DT	rs2886671	Intron	3p14.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CFLAR	rs7558475	Non Coding Transcript Variant	2q33.1	Protective	> 0.01	Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk
CHEK2	-	CNV	22q12.1	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
CHEK2	-	Exon	22q12.1	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
CHEK2	-	Exon	22q12.1	Disease	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
CHEK2	-	Exon	22q12.1	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
CHEK2	rs17879961	Exon	22q12.1	Disease	< 0.01	CHEK2 variant I157T may be associated with increased breast cancer risk
CHEK2	rs555607708	Exon	22q12.1	Disease	< 0.01	Low-penetrance susceptibility to breast cancer due to CHEK2*1100delC in noncarriers of BRCA1 or BRCA2 mutations
CHEK2	rs555607708	Exon	22q12.1	Disease	< 0.01	CHEK2*1100delC and susceptibility to breast cancer: a collaborative analysis involving 10,860 breast cancer cases and 9,065 controls from 10 studies
CHEK2	rs555607708	Exon	22q12.1	Disease	< 0.01	A CHEK2 Genetic Variant Contributing to a Substantial Fraction of Familial Breast Cancer
CHEK2	rs555607708	Exon	22q12.1	Disease	< 0.01	CHEK2*1100delC Genotyping for Clinical Assessment of Breast Cancer Risk: Meta-Analyses of 26,000 Patient Cases and 27,000 Controls
CHIC2	rs368360781	Exon	4q12	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
CHST9	rs1436904	Intron	18q11.2	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
CHST9	rs745983748	Intron	18q11.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CLDN10	rs1325774	3 Prime UTR Variant	13q32.1	Disease	> 0.01	CLDN10 single nucleotide polymorphism rs1325774 alters the risk of breast cancer in south chinese women
CLIP1	rs34292795	Exon	12q24.31	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
CMSS1	rs9833888	Intron	3p12.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
CMSS1	rs35701020	Intron	3q12.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CNTNAP1	rs72826962	Intron	17q21.2	Disease	< 0.01	Association analysis identifies 65 new breast cancer risk loci
CNTRL	rs17292952	Exon	9q33.2	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
COLEC10	rs3102735	Intron	8q24.12	Protective	> 0.01	Risk association of RANKL and OPG gene polymorphism with breast cancer to bone metastasis in Pashtun population of Khyber Pakhtunkhwa, Pakistan
COMT	rs4680	Exon	22q11.21	Disease	> 0.01	Association between polymorphisms in estrogen metabolism genes and breast cancer development in Chinese women: A prospective case-control study
COMT	rs737865	Intron	22q11.21	Protective	> 0.01	Breast Cancer Risk Reduction and Membrane-Bound Catechol O-Methyltransferase Genetic Polymorphisms
COPS2	rs141308737	Intron	15q21.1	Disease	> 0.01	Genetic variants of genes in the NER pathway associated with risk of breast cancer: A large‐scale analysis of 14 published GWAS datasets in the DRIVE study
CREB5	rs17156577	Intron	7p15.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
CTLA4	rs231775	Exon	2q33.2	Protective	> 0.01	Cytotoxic T lymphocyte antigen-4 gene in breast cancer
CTLA4	rs231775	Exon	2q33.2	Disease	> 0.01	Cytotoxic T-lymphocyte antigen 4 polymorphisms and breast cancer susceptibility: Evidence from a meta-analysis
CTNNA2	rs13025833	Intron	2p12	Disease	> 0.01	A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia
CTNNB1	rs4135385	Intron	3p22.1	Disease	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes with Breast Cancer in Saudi Patients
CUX1	rs71559437	Intron	7q22.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
CUX1	rs71559437	Intron	7q22.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CUX1	rs782176246	Exon	7q22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
CUX2	rs11065822	Intron	12q24.11	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
CUX2	rs11065822	Intron	12q24.11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
CYP17A1	rs4919687	Intron	10q24.32	Disease	> 0.01	CYP17 Genetic Variation and Risk of Breast and Prostate Cancer From the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3)
CYP17A1	rs743572	5 Prime UTR Variant	10q24.32	Disease	> 0.01	Association between CYP17 gene polymorphism and risk of breast cancer in young women
CYP19A1	rs10046	3 Prime UTR Variant	15q21.2	Disease	> 0.01	Analysis of CYP17, CYP19 and CYP1A1 Gene Polymorphisms in Iranian Women With Breast Cancer
CYP19A1	rs1008805	Intron	15q21.2	Disease	> 0.01	A CYP19 (aromatase) polymorphism is associated with increased premenopausal breast cancer risk
CYP1A1	rs1048943	Exon	15q24.1	Disease	> 0.01	Polymorphisms of catechol estrogens metabolism pathway genes and breast cancer risk in Mexican women
CYP1A2	rs762551	Intron	15q24.1	Disease	> 0.01	Genetic polymorphisms of estrogen metabolizing enzyme and breast cancer risk in Thai women
CYP1A2	rs762551	Intron	15q24.1	Disease	> 0.01	Estrogen Metabolism-Related Genes and Breast Cancer Risk: The Multiethnic Cohort Study
CYP1A2	rs762551	Intron	15q24.1	Protective	> 0.01	Genetic polymorphism of estrogen metabolizing enzymes in Siberian women with breast cancer
CYP1B1	rs1056836	Exon	2p22.2	Disease	> 0.01	Cytochrome P450 CYP1B1 and catechol O -methyltransferase (COMT ) genetic polymorphisms and breast cancer susceptibility in a Turkish population
CYP1B1	rs1056836	Exon	2p22.2	Protective	> 0.01	Association between polymorphisms in estrogen metabolism genes and breast cancer development in Chinese women: A prospective case-control study
CYP1B1	rs1056836	Exon	2p22.2	Disease	> 0.01	Evaluation of Breast Cancer Risk in a Multigenic Model Including Low Penetrance Genes Involved in Xenobiotic and Estrogen Metabolisms
CYP2B7P	rs3844443	Intron	19q13.2	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
CYP2C19	rs4986893	Exon	10q23.33	Disease	< 0.01	Association of CYP2C19*3 Gene Polymorphism With Breast Cancer in Chinese Women
CYP2D6	rs1065852	Exon	22q13.2	Disease	> 0.01	Detection of Cytochrome P450 Polymorphisms in Breast Cancer Patients May Impact on Tamoxifen Therapy
CYP2D6	rs3892097	Splice Acceptor Variant	22q13.2	Disease	> 0.01	CYP2D6 genotypes in Spanish women with breast cancer
CYP2D6	rs3892097	Splice Acceptor Variant	22q13.2	Disease	> 0.01	Detection of Cytochrome P450 Polymorphisms in Breast Cancer Patients May Impact on Tamoxifen Therapy
CYP3A4	rs2242480	Intron	7q22.1	Disease	> 0.01	Correlations between CYP3A4 polymorphism and susceptibility to breast cancer in Chinese Han population
CYP3A5	rs776746	Splice Acceptor Variant	2p22.2	Disease	> 0.01	Genetic polymorphisms in estrogen metabolism and breast cancer risk in case–control studies in Japanese, Japanese Brazilians and non-Japanese Brazilians
DCC	rs375401214	Exon	18q21.2	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
DCLRE1B	rs11552449	Exon	1p13.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
DCLRE1B	rs11552449	Exon	1p13.2	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
DENND10	rs74157632	Exon	10q26.11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
DESI1	rs2267437	Intron	22q13.2	Disease	> 0.01	Polymorphisms in Nonhomologous End-Joining Genes Associated with Breast Cancer Risk and Chromosomal Radiosensitivity
DIRC3	rs16857609	Intron	2q35	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
DIRC3	rs16857609	Intron	2q35	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
DIRC3	rs16857609	Intron	2q35	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
DKK3	rs6485350	Intron	11p15.3	Protective	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes with Breast Cancer in Saudi Patients
DKK4	rs3763511	Intron	8p11.21	Disease	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes with Breast Cancer in Saudi Patients
DLEU1	rs9316500	Intron	13q14.3	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
DLEU1	rs2286657	Intron	13q14.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
DLX2-DT	rs2016394	Intron	2q31.1	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
DLX2-DT	rs2016394	Intron	2q31.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
DNAH11	rs7971	3 Prime UTR Variant	7p15.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
DNAH11	rs7971	3 Prime UTR Variant	7p15.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
DNAJC15	-	CNV	13q14.11	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
DNMT1	rs16999593	Exon	19p13.2	Disease	> 0.01	Association of DNMT1 and DNMT3B Polymorphisms With Breast Cancer Risk in Han Chinese Women From South China
DNMT1	rs2228612	Exon	19p13.2	Protective	> 0.01	DNMT1 genetic polymorphisms affect breast cancer risk in the central European Caucasian population
DNMT3B	rs2424908	Intron	20q11.21	Protective	> 0.01	Association of DNMT1 and DNMT3B Polymorphisms With Breast Cancer Risk in Han Chinese Women From South China
DOCK1	rs9418690	Intron	10q26.2	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
DRD3	rs167770	Intron	3q13.31	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
DROSHA	rs642321	3 Prime UTR Variant	5p13.3	Disease	> 0.01	Association of DROSHA rs6877842, rs642321 and rs10719 polymorphisms with increased susceptibility to breast cancer: A case-control study with genotype and haplotype analysis
E2F1	-	CNV	20q11.22	Disease	-	E2F1 copy number variations in germline and breast cancer: a retrospective study of 222 Italian women
EBF1	rs1432679	Intron	5q33.3	Protective	> 0.01	Association of multiple genetic variants with breast cancer susceptibility in the Han Chinese population
EBF1	rs1432679	Intron	5q33.3	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
EBF1	rs1432679	Intron	5q33.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
EBF2	rs13256025	Intron	8p21.2	Disease	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
EBF2	rs13256025	Intron	8p21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ECE1-AS1	rs213051	Intron	1p36.12	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
ECE1	rs213051	Intron	1p36.12	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
ECHDC1	rs6569480	Intron	6q22.33	Disease	> 0.01	Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
ECHDC1	rs7776136	Intron	6q22.33	Disease	> 0.01	Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
EHMT1	rs3125795	Intron	9q34.3	Disease	> 0.01	Genetic variants in epigenetic genes and breast cancer risk
EHMT1	rs4634736	Intron	9q34.3	Protective	> 0.01	Genetic variants in epigenetic genes and breast cancer risk
EHMT2	rs535586	Exon	6p21.33	Disease	> 0.01	Genetic variants in epigenetic genes and breast cancer risk
EI24	rs2155388	Intron	3q23	Disease	> 0.01	Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer
EIF4E	rs141689493	Intron	4q23	Disease	< 0.01	Association of breast cancer risk and the mTOR pathway in women of African ancestry in ‘The Root’ Consortium
ELL	rs1469412	Intron	19p13.11	Protective	> 0.01	Genetic variants of genes in the NER pathway associated with risk of breast cancer: A large‐scale analysis of 14 published GWAS datasets in the DRIVE study
ELL	rs4808801	Intron	19p13.11	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
ELL	rs8105994	Intron	19p13.11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ELN-AS1	rs17855988	Intron	7q11.23	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
ELN	rs17855988	Exon	7q11.23	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
EMBP1	rs11249433	Intron	1p11.2	Disease	> 0.01	Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus
EMBP1	rs11249433	Intron	1p11.2	Disease	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
EMBP1	rs11249433	Intron	1p11.2	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
EMBP1	rs11249433	Intron	1p11.2	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
EMBP1	rs11249433	Intron	1p11.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
EMID1	rs132390	Intron	22q12.2	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
EMID1	rs132390	Intron	22q12.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
EMX2OS	rs2901157	Intron	10q26.11	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
EMX2OS	rs2901157	Intron	10q26.11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
EPCAM	rs1126497	Exon	2p21	Disease	> 0.01	A non-synonymous polymorphism Thr115Met in the EpCAM gene is associated with an increased risk of breast cancer in Chinese population
EPHX1	rs1051740	Exon	1q42.12	Protective	> 0.01	A Systematic Approach to Analysing Gene-Gene Interactions: Polymorphisms at the Microsomal Epoxide Hydrolase EPHX and Glutathione S-transferase GSTM1, GSTT1, and GSTP1 Loci and Breast Cancer Risk
EPHX1	rs1051740	Exon	1q42.12	Disease	> 0.01	Implication of Xenobiotic Metabolizing Enzyme gene (CYP2E1, CYP2C19, CYP2D6, mEH and NAT2) Polymorphisms in Breast Carcinoma
ERBB2	rs1136201	Exon	17q12	Disease	> 0.01	Population-Based, Case-Control Study of HER2 Genetic Polymorphism and Breast Cancer Risk
ERBB2	rs1136201	Exon	17q12	Disease	> 0.01	HER2 polymorphism and breast cancer risk in Portugal
ERBB2	rs1136201	Exon	17q12	Disease	> 0.01	Association between the Arg72Pro Genotypes in the TP53 Gene and Ile655Val in the HER2 Gene and the Risk of Developing Breast Cancer in the Population of Amapá, Northern Brazil
ERBB2	rs1801201	Exon	17q12	Disease	< 0.01	The rare ERBB2 variant Ile654Val is associated with an increased familial breast cancer risk
ERBB3	rs773123	Exon	12q13.2	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
ERBB4	rs13393577	Intron	2q34	Disease	> 0.01	A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study
ERCC1	rs11615	Exon	19q13.32	Disease	> 0.01	Polymorphisms in the ERCC1 and XPF Genes and Risk of Breast Cancer in a Chinese Population
ERCC1	rs11615	Exon	19q13.32	Disease	> 0.01	Nucleotide excision repair pathway gene polymorphisms are linked to breast cancer risk in a Chinese population
ERCC2	rs1799793	Exon	19q13.32	Disease	> 0.01	Significant association between ERCC2 and MTHR polymorphisms and breast cancer susceptibility in Moroccan population: genotype and haplotype analysis in a case-control study
ERCC2	rs1799793	Exon	19q13.32	Disease	> 0.01	Analysis of ERCC1 and ERCC2 gene variants in osteosarcoma, colorectal and breast cancer
ERCC2	rs50872	Intron	19q13.32	Disease	> 0.01	Nucleotide excision repair pathway gene polymorphisms are linked to breast cancer risk in a Chinese population
ERCC2	rs13181	Exon	19q13.32	Disease	> 0.01	Involvement of ERCC1 (rs3212986) and ERCC2 (rs1799793, rs13181) polymorphisms of DNA repair genes in breast cancer occurrence in Burkina Faso
ERCC4	rs1800067	Exon	16p13.12	Disease	> 0.01	Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk
ERCC4	rs744154	Intron	16p13.12	Protective	> 0.01	ERCC4 Associated with Breast Cancer Risk: A Two-Stage Case-Control Study Using High-throughput Genotyping
ERCC5	rs17655	Exon	13q33.1	Disease	> 0.01	Synergistic Effects of Polymorphisms in DNA Repair Genes and Endogenous Estrogen Exposure on Female Breast Cancer Risk
ERCC5	rs17655	Exon	13q33.1	Disease	> 0.01	The interplay between XPG-Asp1104His polymorphism and reproductive risk factors elevates risk of breast cancer in Tanzanian women: A multiple interaction analysis
ESR1	rs2228480	Exon	6q25.1-q25.2	Protective	> 0.01	Evaluation of functional genetic variants at 6q25.1 and risk of breast cancer in a Chinese population
ESR1	rs2747652	Intron	6q25.1-q25.2	Disease	> 0.01	Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
ESR1	rs2747652	Intron	6q25.1	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
ESR1	rs3798758	Intron	6q25.1-q25.2	Disease	> 0.01	Evaluation of functional genetic variants at 6q25.1 and risk of breast cancer in a Chinese population
ESR1	rs851984	Intron	6q25.1-q25.2	Disease	> 0.01	Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
ESR1	rs9918437	Intron	6q25.1-q25.2	Disease	> 0.01	Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
ESR1	rs910416	Intron	6q25.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ESR2	rs2987983	Intron	14q23.3	Disease	> 0.01	Genetic polymorphisms of ESR1, ESR2, CYP17A1, and CYP19A1 and the risk of breast cancer: a case control study from North India
ESR2	rs2987983	Intron	14q23.3	Disease	> 0.01	Polymorphisms in the promoter region of ESR2 gene and breast cancer susceptibility
ESRRG	rs11117758	Intron	1q41	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ESRRG	rs11117758	Intron	1q41	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
EXO1	rs72755295	Intron	1q43	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
EXO1	rs4149991	Intron	1q43	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
FAM126B	rs114962751	Intron	2q33.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
FAM72B	-	-	1p11.2	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
FANCC	-	Exon	9q22.32	Disease	< 0.01	Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles
FANCC	-	Exon	9q22.32	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
FANCD2	rs201811817	Splice Donor Variant	3p25.3	Disease	< 0.01	Case-control analysis of truncating mutations in DNA damage response genes connects TEX15 and FANCD2 with hereditary breast cancer susceptibility
FANCM	-	Exon	14q21.2	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
FANCM	-	Exon	14q21.2	Disease	< 0.01	Association Between Loss-of-Function Mutations Within the FANCM Gene and Early-Onset Familial Breast Cancer
FANCM	-	Exon	14q21.2	Disease	-	FANCM missense variants and breast cancer risk: a case-control association study of 75,156 European women
FANCM	rs144567652	Exon	14q21.2	Disease	< 0.01	FANCM Mutation c.5791C>T Is a Risk Factor for Triple-Negative Breast Cancer in the Finnish Population
FANCM	rs144567652	Exon	14q21.2	Disease	< 0.01	The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer
FANCM	rs144567652	Exon	14q21.2	Disease	< 0.01	FANCM c.5791C>T nonsense mutation (rs144567652) induces exon skipping, affects DNA repair activity and is a familial breast cancer risk factor
FANCM	rs147021911	Exon	14q21.2	Disease	< 0.01	Exome Sequencing Identifies FANCM as a Susceptibility Gene for Triple-Negative Breast Cancer
FANCM	rs368728266	Exon	14q21.2	Disease	< 0.01	The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer
FAS	rs1800682	Intron	10q23.31	Disease	> 0.01	Functional Polymorphisms of FAS and FASL Gene and Risk of Breast Cancer – Pilot Study of 134 Cases
FAS	rs2234767	Exon	10q23.31	Disease	> 0.01	Polymorphisms of the FAS and FASL genes and risk of breast cancer
FASLG	rs5030772	Intron	1q24.3	Disease	> 0.01	Functional Polymorphisms of FAS and FASL Gene and Risk of Breast Cancer – Pilot Study of 134 Cases
FBLN2	rs556004379	Exon	3p25.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
FGFR2	-	-	10q26.13	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
FGFR2	-	Exon	10q26.13	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
FGFR2	rs1078806	Intron	10q26.13	Disease	> 0.01	Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
FGFR2	rs2981578	Intron	10q26.13	Disease	> 0.01	Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1
FGFR2	rs2981579	Intron	10q26.13	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
FGFR2	rs2981582	Intron	10q26.13	Disease	> 0.01	Low penetrance alleles as risk modifiers in familial and sporadic breast cancer
FGFR2	rs2981582	Intron	10q26.13	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
FGFR2	rs2981582	Intron	10q26.13	Disease	> 0.01	Evaluation of the Association between FGFR2 Gene Polymorphisms and Breast Cancer Risk in the Bangladeshi Population
FGFR2	rs35054928	Intron	10q26.13	Disease	> 0.01	Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1
FGFR2	rs45631563	Intron	10q26.13	Protective	> 0.01	Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1
FGFR2	rs1219648	Intron	10q26.13	Disease	> 0.01	Evaluation of the Association between FGFR2 Gene Polymorphisms and Breast Cancer Risk in the Bangladeshi Population
FGFR2	rs2981579	Intron	10q26.13	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
FGFR2	rs2981579	Intron	10q26.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
FGGY	rs7520470	Intron	1p32.1	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
FILIP1L	rs9833888	Intron	3p12.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
FILIP1L	rs35701020	Intron	3q12.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
FLACC1	rs1830298	Intron	2q33.1	Disease	> 0.01	Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk
FMNL3	-	-	12q13.12	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
FOXP1	rs6805189	Intron	3p13	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
FOXP1	rs6805189	Intron	3p13	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
FOXP3	rs3761548	Intron	Xp11.23	Disease	> 0.01	Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women
FRZB	rs7775	Exon	2q32.1	Protective	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes with Breast Cancer in Saudi Patients
FTO	rs11075995	Intron	16q12.2	Disease	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
FTO	rs11075995	Intron	16q12.2	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
FTO	rs11075995	Intron	16q12.2	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
FTO	rs17817449	Intron	16q12.2	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
FTO	rs17817449	Intron	16q12.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
FTO	rs9939609	Intron	16q12.2	Protective	> 0.01	Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry
FTO	rs62048402	Intron	16q12.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GAREM1	rs117618124	Intron	18q12.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
GAREM1	rs72931898	Intron	18q12.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GATA3	rs570613	Intron	10p14	Protective	> 0.01	Common Genetic Variation in GATA-Binding Protein 3 and Differential Susceptibility to Breast Cancer by Estrogen Receptor α Tumor Status
GATAD2A	rs2965183	Intron	19p13.11	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
GATAD2A	rs4808961	Intron	19p13.11	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GH1	rs6173	5 Prime UTR Variant	17q23.3	Protective	> 0.01	Association of polymorphisms and haplotypes in the human growth hormone 1 (GH1) gene with breast cancer
GIPR	rs71338792	Intron	19q13.32	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
GIPR	rs61373376	Intron	19q13.32	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GLO1	rs4746	Exon	6p21.2	Disease	> 0.01	CYP17, GSTP1, PON1 and GLO1 gene polymorphisms as risk factors for breast cancer: an Italian case-control study
GNAS-AS1	rs563844600	Intron	20q13.32	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
GNAS	rs563844600	Exon	20q13.32	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
GPC1-AS1	rs2292832	Intron	2q37.3	Disease	> 0.01	The association between genetic variation rs2292832 and the processing efficiency of pre-mir-149 affects the risk of breast cancer
GPC1	rs2292832	Intron	2q37.3	Disease	> 0.01	The association between genetic variation rs2292832 and the processing efficiency of pre-mir-149 affects the risk of breast cancer
GPR19	rs34330	5 Prime UTR Variant	12p13.1	Disease	> 0.01	Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
GPRIN2	rs4445576	Exon	10q11.22	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
GPX1	rs1050450	Exon	3p21.31	Disease	> 0.01	Associations between GPX1 Pro198Leu polymorphism, erythrocyte GPX activity, alcohol consumption and breast cancer risk in a prospective cohort study
GPX1	rs1050450	Exon	3p21.31	Disease	> 0.01	Association between Polymorphisms in Glutathione Peroxidase and Selenoprotein P Genes, Glutathione Peroxidase Activity, HRT Use and Breast Cancer Risk
GRHL1	rs113577745	Intron	2p25.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
GRHL1	rs539902477	Intron	2p25.1	Disease	< 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GRIA4	-	Exon	11q22.3	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
GRM7	rs7610073	Intron	3p26.1	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Allelotype Influence at Glutathione S-transferase M1 Locus on Breast Cancer Susceptibility
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Association between polymorphisms of glutathione S-transferase genes (GSTM1, GSTP1 and GSTT1) and breast cancer risk in a sample Iranian population
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Polymorphisms in GSTM1, GSTT1, GSTP1, and GSTM3 Genes and Breast Cancer Risk in Northeastern Mexico
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Glutathione S-transferase M1, T1, and P1 Genotypes and Breast Cancer Risk: A Study in a Portuguese Population
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Influence of germline polymorphisms of GSTT1, GSTM1, and GSTP1 in familial versus sporadic breast cancer susceptibility and survival
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	A functional polymorphism in the promoter region of GSTM1 implies a complex role for GSTM1 in breast cancer
GSTM1	PseudoSNP for CNV - rs366631	CNV deletion	1p13.3	Disease	> 0.01	Investigating the Role of Glutathione S- Transferase Genes, Histopathological and Molecular Subtypes, Gene-Gene Interaction and Its Susceptibility to Breast Carcinoma in Ethnic North- Indian Population
GSTM2	rs1245957540	Intron	1p13.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
GSTO1	rs4925	Exon	10q25.1	Disease	> 0.01	Association of GSTO1 A140D and GSTO2 N142D Gene Variations with Breast Cancer Risk
GSTO2	rs156697	Exon	10q25.1	Disease	> 0.01	Association of GSTO1 A140D and GSTO2 N142D Gene Variations with Breast Cancer Risk
GSTP1	rs1695	Exon	11q13.2	Disease	> 0.01	Cruciferous vegetables, the GSTP1 Ile105Val genetic polymorphism, and breast cancer risk
GSTP1	rs1695	Exon	11q13.2	Disease	> 0.01	The GSTP1 105Val Allele Increases Breast Cancer Risk and Aggressiveness but Enhances Response to Cyclophosphamide Chemotherapy in North China
GSTP1	rs1695	Exon	11q13.2	Disease	> 0.01	Polymorphisms of catechol estrogens metabolism pathway genes and breast cancer risk in Mexican women
GSTP1	rs1695	Exon	11q13.2	Disease	> 0.01	Association between polymorphisms of glutathione S-transferase genes (GSTM1, GSTP1 and GSTT1) and breast cancer risk in a sample Iranian population
GSTP1	rs1695	Exon	11q13.2	Disease	> 0.01	Association between polymorphisms in estrogen metabolism genes and breast cancer development in Chinese women: A prospective case-control study
GSTP1	rs1695	Exon	11q13.2	Protective	> 0.01	Investigating the Role of Glutathione S- Transferase Genes, Histopathological and Molecular Subtypes, Gene-Gene Interaction and Its Susceptibility to Breast Carcinoma in Ethnic North- Indian Population
GSTT1	-	Gene deletion	22q11.23	Disease	> 0.01	Glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) variants and breast cancer risk in Burkina Faso
GSTT1	-	Gene deletion	22q11.23	Disease	> 0.01	Glutathione S-transferases (GSTT1 and GSTM1) gene deletions in Tunisians: susceptibility and prognostic implications in breast carcinoma
GSTT1	-	Gene deletion	22q11.23	Disease	> 0.01	Glutathione S-transferase M1, T1, and P1 Genotypes and Breast Cancer Risk: A Study in a Portuguese Population
GSTT1	-	Gene deletion	22q11.23	Disease	> 0.01	Influence of germline polymorphisms of GSTT1, GSTM1, and GSTP1 in familial versus sporadic breast cancer susceptibility and survival
GSTT1	-	Gene deletion	22q11.23	Disease	> 0.01	Glutathione S-Transferase T1 and M1 Gene Polymorphisms among Breast Cancer Susceptible Ghanaians
GTF2H4	rs1264308	Intron	6p21.33	Protective	> 0.01	Genetic variants of genes in the NER pathway associated with risk of breast cancer: A large‐scale analysis of 14 published GWAS datasets in the DRIVE study
H19	rs2107425	Intron	11p15.5	Protective	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
H19	rs217727	Non Coding Transcript Variant	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
H19	rs2839698	Non Coding Transcript Variant	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
H19	rs3741219	Non Coding Transcript Variant	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
H3-3A	rs749423281	Exon	1q42.12	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HCN1	rs981782	Intron	5p12	Disease	> 0.01	Association of multiple genetic variants with breast cancer susceptibility in the Han Chinese population
HCN1	rs981782	Intron	5p12	Protective	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
HELQ	rs10718573	Intron	4q21.23	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
HIF1A	rs11549465	Exon	14q23.2	Disease	> 0.01	Associations Between Hypoxia-Inducible factor-1alpha (HIF-1alpha) Gene Polymorphisms and Risk of Developing Breast Cancer
HIF1A	rs11549465	Exon	14q23.2	Disease	> 0.01	SNP 1772 C > T of HIF-1α gene associates with breast cancer risk in a Taiwanese population
HIF1A	rs11549467	Exon	14q23.2	Disease	< 0.01	Polymorphisms in HIFs and Breast Cancer Sutarsceptibility in Chinese Women: A Case-Control Study
HIF1A	rs142179458	Exon	14q23.2	Disease	< 0.01	Identification of Novel Breast Cancer Risk Loci
HIF1A-AS3	rs11549465	Intron	14q23.2	Disease	> 0.01	Associations Between Hypoxia-Inducible factor-1alpha (HIF-1alpha) Gene Polymorphisms and Risk of Developing Breast Cancer
HIF1A-AS3	rs11549465	Intron	14q23.2	Disease	> 0.01	SNP 1772 C > T of HIF-1α gene associates with breast cancer risk in a Taiwanese population
HIF1A-AS3	rs11549467	Intron	14q23.2	Disease	< 0.01	Polymorphisms in HIFs and Breast Cancer Sutarsceptibility in Chinese Women: A Case-Control Study
HIF1A-AS3	rs142179458	Intron	14q23.2	Disease	< 0.01	Identification of Novel Breast Cancer Risk Loci
HIVEP3	rs79724016	Intron	1p34.2	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
HIVEP3	rs10749837	Intron	1p34.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
HLA-A	rs369261720	Exon	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-A	rs41548917	Exon	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-A	rs41562120	Exon	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-A	rs756231831	Exon	6p22.1	Disease	-	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-A	rs372503438	Exon	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-A	rs758168864	Exon	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-B	rs9266183	Exon	6p21.33	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-DRB1	rs17885222	Exon	6p21.32	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-DRB1	rs756741350	Exon	6p21.32	Disease	-	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-DRB1	rs769556955	Exon	6p21.32	Disease	-	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
HLA-G	rs1063320	3 Prime UTR Variant	6p22.1	Protective	> 0.01	3'UTR-HLA-G polymorphisms and circulating sHLA-G are associated with breast cancer: Evidence from a meta-analysis
HLA-G	rs371194629	3 Prime UTR Variant	6p22.1	Disease	> 0.01	3'UTR-HLA-G polymorphisms and circulating sHLA-G are associated with breast cancer: Evidence from a meta-analysis
HMMR	rs10515860	Intron	5q34	Disease	> 0.01	Network modeling links breast cancer susceptibility and centrosome dysfunction
HMMR-AS1	rs10515860	Intron	5q34	Disease	> 0.01	Network modeling links breast cancer susceptibility and centrosome dysfunction
HNF4G	rs2943559	Intron	8q21.13	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
HOXB13	rs138213197	Exon	17q21.32	Disease	< 0.01	Association of a HOXB13 Variant with Breast Cancer
HSD11B1	rs11807619	Intron	1q32.2	Disease	> 0.01	Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II
HSD11B1	rs932335	Intron	1q32.2	Disease	> 0.01	Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II
HSD11B1-AS1	rs11807619	Intron	1q32.2	Disease	> 0.01	Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II
HSD11B1-AS1	rs932335	Intron	1q32.2	Disease	> 0.01	Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II
HSD17B1	rs605059	Exon	17q21.2	Disease	> 0.01	African American-preponderant single nucleotide polymorphisms (SNPs) and risk of breast cancer
HSD17B14	-	CNV deletion	19q13.33	Disease	< 0.01	Exome sequencing identified rare recurrent copy number variants and hereditary breast cancer susceptibility
HSPA1A	rs1061581	Exon	14q23.3	Disease	> 0.01	Genetic Variation in the Tumor Necrosis Factor-Alpha Promoter Region and in the Stress Protein hsp70-2: Susceptibility and Prognostic Implications in Breast Carcinoma
HSPA4	rs6596100	Intron	5q31.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
HSPA4	rs571173399	3 Prime UTR Variant	5q31.1	Protective	< 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
HUS1	rs1056663	Exon	7p12.3	Disease	> 0.01	Low penetrance alleles as risk modifiers in familial and sporadic breast cancer
HUS1	rs2708861	Intron	7p12.3	Disease	> 0.01	Low penetrance alleles as risk modifiers in familial and sporadic breast cancer
ICAM1	rs5498	Exon	19p13.2	Disease	> 0.01	Large-Scale Association Study Identifies ICAM Gene Region as Breast and Prostate Cancer Susceptibility Locus
ICAM5	rs1056538	Exon	19p13.2	Disease	> 0.01	Large-Scale Association Study Identifies ICAM Gene Region as Breast and Prostate Cancer Susceptibility Locus
ICAM5	rs281439	Non Coding Transcript Variant	19p13.2	Disease	> 0.01	Large-Scale Association Study Identifies ICAM Gene Region as Breast and Prostate Cancer Susceptibility Locus
IFNG	rs2430561	Intron	21q22.11	Disease	> 0.01	Tumor Necrosis Factor Alpha and Beta and Interferon Gamma Gene Polymorphisms in Turkish Breast Cancer Patients
IFNG	rs2430561	Intron	21q22.11	Disease	> 0.01	Polymorphism in the genes of alpha and beta tumor necrosis factors (TNF-α and TNF-β) and gamma interferon (IFN-γ) among Iranian women with breast cancer
IGF1	rs1019731	Intron	12q23.2	Protective	> 0.01	Polymorphisms of Insulin-Like Growth Factor 1 Pathway Genes and Breast Cancer Risk
IGF1	rs12821878	Intron	12q23.2	Protective	> 0.01	Polymorphisms of Insulin-Like Growth Factor 1 Pathway Genes and Breast Cancer Risk
IGF1	rs1520220	Intron	12q23.2	Disease	> 0.01	IGF1 and IGFBP3 tagging polymorphisms are associated with circulating levels of IGF1, IGFBP3 and risk of breast cancer
IGF1	rs2162679	Intron	12q23.2	Protective	> 0.01	Polymorphisms of genes coding for insulin-like growth factor 1 and its major binding proteins, circulating levels of IGF-I and IGFBP-3 and breast cancer risk: results from the EPIC study
IGF2BP2	rs4402960	Intron	3q27.2	Disease	> 0.01	Correlation Between IGF2BP2 Gene Polymorphism and the Risk of Breast Cancer in Chinese Han Women
IGF2BP2	rs4402960	Intron	3q27.2	Disease	> 0.01	Novel Association of IGF2BP2 Gene Variants With Altered Risk of Breast Cancer and as Potential Molecular Biomarker of Triple Negative Breast Cancer
IGFBP-AS1	rs4442975	Intron	2q35	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
IL18	rs549908	Exon	11q23.1	Protective	> 0.01	Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer
IL19	rs1800871	Intron	1q32.1	Disease	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
IL19	rs1800872	Intron	1q32.1	Disease	> 0.01	Association of the IL-10 gene rs1800872 (-592 C>A) polymorphism with breast cancer in a Mexican population
IL19	rs1800896	Intron	1q32.1	Disease	> 0.01	Polymorphic variations in IL-1β, IL-6 and IL-10 genes, their circulating serum levels and breast cancer risk in Indian women
IL19	rs1800896	Intron	1q32.1	Disease	> 0.01	Association of interleukin-10 polymorphisms and haplotypes with the risk of breast cancer in northern China
IL1B	rs1143627	5 Prime UTR Variant	2q14.1	Disease	> 0.01	The Correlation between IL-1β-C31T Gene Polymorphism and Susceptibility to Breast Cancer
IL1B	rs1143634	Exon	2q14.1	Disease	> 0.01	Polymorphic variations in IL-1β, IL-6 and IL-10 genes, their circulating serum levels and breast cancer risk in Indian women
IL1R1	rs10490571	Intron	2q11.2-q12.1	Disease	> 0.01	Interleukin gene polymorphisms in Chinese Han population with breast cancer, a case-control study
IL1RN	rs2234663	Intron	2q14.1	Protective	> 0.01	Association between interleukin-1 receptor antagonist (IL-1ra) VNTR, gene polymorphism and breast cancer susceptibility in Iranian population: Experimental and web-based analysis
IL1RN	rs315919	Intron	2q14.1	Protective	> 0.01	IL‐1RN gene polymorphisms are associated with breast cancer risk in a Chinese Han population
IL1RN	rs3181052	Intron	2q14.1	Protective	> 0.01	IL‐1RN gene polymorphisms are associated with breast cancer risk in a Chinese Han population
IL1RN	rs4252019	Intron	2q14.1	Protective	> 0.01	IL‐1RN gene polymorphisms are associated with breast cancer risk in a Chinese Han population
IL1RN	rs452204	Intron	2q14.1	Protective	> 0.01	IL‐1RN gene polymorphisms are associated with breast cancer risk in a Chinese Han population
IL1RN	rs928940	Intron	2q14.1	Protective	> 0.01	IL‐1RN gene polymorphisms are associated with breast cancer risk in a Chinese Han population
IL6	rs1800795	Intron	7p15.3	Protective	> 0.01	Polymorphic variations in IL-1β, IL-6 and IL-10 genes, their circulating serum levels and breast cancer risk in Indian women
IL6-AS1	rs1800795	Intron	7p15.3	Protective	> 0.01	Polymorphic variations in IL-1β, IL-6 and IL-10 genes, their circulating serum levels and breast cancer risk in Indian women
IL6-AS1	rs1800795	Intron	7p15.3	Disease	> 0.01	Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer
IL6-AS1	rs1800796	Non Coding Transcript Variant	7p15.3	Protective	> 0.01	Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer
IL6-AS1	rs1800797	Non Coding Transcript Variant	7p15.3	Disease	> 0.01	Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer
INSL6	rs56118985	Intron	9p24.1	Disease	< 0.01	Identification of Novel Breast Cancer Risk Loci
INSR	rs1799817	Exon	19p13.2	Protective	> 0.01	Nested case-control study of energy regulation candidate gene single nucleotide polymorphisms and breast cancer
IRF1-AS1	rs2522057	Intron	5q31.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
IRS2	rs2289046	3 Prime UTR Variant	13q34	Protective	> 0.01	Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II
ISX	rs8140287	Exon	22q12.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
ITGA2	rs1801106	Exon	5q11.2	Disease	> 0.01	Integrin alpha-2 and beta-3 gene polymorphisms and breast cancer risk
ITGB3	rs5918	Exon	17q21.32	Disease	> 0.01	Integrin beta3 Leu33Pro polymorphism and breast cancer risk: a population-based case-control study in Germany
ITPR1	rs6762644	Intron	3p26.1	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
ITPR1	rs6762558	Intron	3p26.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ITPR2	rs4964006	Intron	12p11.23	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
ITPR3	rs2229642	Exon	6p21.31	Disease	> 0.01	Inositol 1,4,5-trisphosphate receptor gene variants are related to the risk of breast cancer in a Chinese population
Intergenic	-	Intergenic	11q13.3	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
Intergenic	-	Intergenic	15q11.2	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
Intergenic	-	Intergenic	16q24.1	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
Intergenic	rs1027113	Intergenic	12p11.22	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs10472076	Intergenic	5q11.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs10474352	Intergenic	5q14.3	Disease	> 0.01	Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.2
Intergenic	rs10484919	Intergenic	6q25.1	Disease	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
Intergenic	rs10637593	Intergenic	2p23.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs10759243	Intergenic	9q31.2	Disease	> 0.01	Association of multiple genetic variants with breast cancer susceptibility in the Han Chinese population
Intergenic	rs10759243	Intergenic	9q31.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs10771399	Intergenic	12p11.22	Protective	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
Intergenic	rs10771399	Intergenic	12p11.22	Protective	> 0.01	Genome-wide association analysis identifies three new breast cancer susceptibility loci
Intergenic	rs10771399	Intergenic	12p11.22	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs10814138	Intergenic	9p13.3	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs10894076	Intergenic	11q24.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs10895304	Intergenic	11q22.2	Disease	> 0.01	Common MMP-7 Polymorphisms and Breast Cancer Susceptibility: A Multistage Study of Association and Functionality
Intergenic	rs10941679	Intergenic	5p12	Disease	> 0.01	Common variants on chromosome 5p12 confer susceptibility to estrogen receptor–positive breast cancer
Intergenic	rs10941679	Intergenic	5p12	Disease	> 0.01	Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation
Intergenic	rs10941679	Intergenic	5p12	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs10941679	Intergenic	5p12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs10995201	Intergenic	10q21.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs11155804	Intergenic	6q25.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs11199914	Intergenic	10q26.12	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs11242675	Intergenic	6p25.3	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs11264454	Intergenic	1q22	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs113701136	Intergenic	19q12	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Intergenic	rs113778879	Intergenic	5q12.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs11568820	Intergenic	12q13.11	Protective	> 0.01	Associations of vitamin D receptor encoding gene variants with premenopausal breast cancer risk
Intergenic	rs11570443	Intergenic	17q21.32	Disease	< 0.01	Association between polymorphisms in cdc27 and breast cancer in a Chinese population
Intergenic	rs11588271	Intergenic	1p32.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs116426014	Intergenic	8p23.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs1167362	Intergenic	12q24.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs11684853	Intergenic	2p24.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs11780156	Intergenic	8q24.21	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs11801299	Intergenic	1q12	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
Intergenic	rs11814448	Intergenic	10p12.31	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs11820646	Intergenic	11q24.3	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs11903787	Intergenic	2q14.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs12118297	Intergenic	1p22.3	Protective	> 0.01	Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci
Intergenic	rs12184413	Intergenic	11q22.2	Protective	> 0.01	Common MMP-7 Polymorphisms and Breast Cancer Susceptibility: A Multistage Study of Association and Functionality
Intergenic	rs12250948	Intergenic	10q25.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12335941	Intergenic	9p21.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12422552	Intergenic	12p13.1	Disease	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
Intergenic	rs12422552	Intergenic	12p13.1	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs12422552	Intergenic	12p13.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12422933	Intergenic	12q24.21	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12479355	Intergenic	2q36.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs12479355	Intergenic	2q36.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12519859	Intergenic	5p13.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12710696	Intergenic	2p24.2-p24.1	Disease	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
Intergenic	rs12710696	Intergenic	2p24.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs12710696	Intergenic	2p24.1	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Intergenic	rs12710696	Intergenic	2p24.1	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs12711947	Intergenic	2q14.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12763451	Intergenic	10p15.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs12870942	Intergenic	13q22.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs12888245	Intergenic	14q11.2	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs12962334	Intergenic	18q11.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs13074711	Intergenic	3q26.31	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
Intergenic	rs13162653	Intergenic	5p15.1	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
Intergenic	rs13365225	Intergenic	8p11.23	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
Intergenic	rs140850326	Intergenic	1p32.3	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs1429142	Intergenic	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
Intergenic	rs1550623	Intergenic	2q31.1	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs1550623	Intergenic	2q31.1	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs17167576	Intergenic	7p21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs17181761	Intergenic	13q22.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs17181761	Intergenic	13q22.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs17356907	Intergenic	12q22	Protective	> 0.01	Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer
Intergenic	rs17356907	Intergenic	12q22	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs17356907	Intergenic	12q22	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs17426269	Intergenic	1p22.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs17513613	Intergenic	19q12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs17529111	Intergenic	6q14.1	Disease	> 0.01	Evaluating Genome-Wide Association Study-Identified Breast Cancer Risk Variants in African-American Women
Intergenic	rs17529111	Intergenic	6q14.1	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs1800629	Intergenic	6p21.33	Protective	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
Intergenic	rs187238	Intergenic	11q23.1	Protective	> 0.01	Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer
Intergenic	rs187238	Intergenic	11q23.1	Disease	> 0.01	Associations between single-nucleotide polymorphisms of the interleukin-18 gene and breast cancer in Iraqi women
Intergenic	rs188686860	Intergenic	2q33.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs1895449	Intergenic	5q14.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs190843378	Intergenic	2q35	Protective	> 0.01	Association of breast cancer risk and the mTOR pathway in women of African ancestry in ‘The Root’ Consortium
Intergenic	rs1946518	Intergenic	11q23.1	Disease	> 0.01	Associations between single-nucleotide polymorphisms of the interleukin-18 gene and breast cancer in Iraqi women
Intergenic	rs1972372	Intergenic	14q11.2	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs2010610	Intergenic	2q14.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs202049448	Intergenic	12q21.31	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs202049448	Intergenic	12q21.31	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs204247	Intergenic	6p23	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs2069429	Intergenic	5q13.2	Disease	> 0.01	Association Study of Germline Variants in CCNB1 and CDK1 with Breast Cancer Susceptibility, Progression, and Survival among Chinese Han Women
Intergenic	rs206966	Intergenic	12q24.31	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs2132572	Intergenic	7p12.3	Disease	> 0.01	IGF1 and IGFBP3 tagging polymorphisms are associated with circulating levels of IGF1, IGFBP3 and risk of breast cancer
Intergenic	rs2181965	Intergenic	13q22.1	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs2188648	Intergenic	7q21.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs2233406	Intergenic	14q13.2	Protective	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
Intergenic	rs2302019	Intergenic	7p14.3	Protective	> 0.01	Polymorphisms in genes involved in GH1 release and their association with breast cancer risk
Intergenic	rs2380205	Intergenic	10p15.1	Disease	> 0.01	A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study
Intergenic	rs2380205	Intergenic	10p15.1	Protective	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
Intergenic	rs2403907	Intergenic	21q21.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs2594714	Intergenic	19p13.13	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs2736108	Intergenic	5p15.33	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs2823093	Intergenic	21q21.1	Protective	> 0.01	Genome-wide association analysis identifies three new breast cancer susceptibility loci
Intergenic	rs2853669	Intergenic	5p15.33	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs2854744	Intergenic	7p12.3	Disease	> 0.01	Polymorphisms in the IGF-1 and IGFBP3 promoter and the risk of breast cancer
Intergenic	rs2854744	Intergenic	7p12.3	Disease	> 0.01	Impact of the IGFBP3 A-202C polymorphism on susceptibility and clinicopathologic features of breast cancer
Intergenic	rs2992756	Intergenic	1p36.13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs2992756	Intergenic	1p36.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs30099	Intergenic	5q11.2	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
Intergenic	rs3087243	Intergenic	2q33.2	Disease	> 0.01	Cytotoxic T-lymphocyte antigen 4 polymorphisms and breast cancer susceptibility: Evidence from a meta-analysis
Intergenic	rs3215401	Intergenic	5p15.33	Protective	> 0.01	Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer
Intergenic	rs34197572	Intergenic	19p13.2	Disease	> 0.01	KEAP1 Genetic Polymorphisms Associate with Breast Cancer Risk and Survival Outcomes
Intergenic	rs34753522	Intergenic	20q12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs35781392	Intergenic	10p14	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs35951924	Intergenic	5q11.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs35951924	Intergenic	5q11.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs361525	Intergenic	6p21.33	Disease	> 0.01	Genetic variation in tumor necrosis factor and lymphotoxin-alpha (TNF–LTA) and breast cancer risk
Intergenic	rs361525	Intergenic	6p21.33	Protective	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
Intergenic	rs36194942	Intergenic	18q12.1	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Intergenic	rs3760982	Intergenic	19q13.31	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs3809114	Intergenic	12q13.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs3903072	Intergenic	11q13.1	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs3928337	Intergenic	14q11.2	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs405447	Intergenic	6p23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4073	Intergenic	4q13.3	Protective	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
Intergenic	rs4233486	Intergenic	1p34.2	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs4233486	Intergenic	1p34.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4322600	Intergenic	14q31.3	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
Intergenic	rs4415084	Intergenic	5p12	Disease	> 0.01	Common variants on chromosome 5p12 confer susceptibility to estrogen receptor–positive breast cancer
Intergenic	rs4415084	Intergenic	5p12	Disease	> 0.01	LncRNA-SNPs in a Brazilian Breast Cancer Cohort: A Case-Control Study
Intergenic	rs4496150	Intergenic	16q24.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4516035	Intergenic	12q13.11	Disease	> 0.01	Associations of vitamin D receptor encoding gene variants with premenopausal breast cancer risk
Intergenic	rs4553808	Intergenic	2q33.2	Disease	> 0.01	Cytotoxic T-lymphocyte antigen 4 polymorphisms and breast cancer susceptibility: Evidence from a meta-analysis
Intergenic	rs4562056	Intergenic	5q35.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs4609972	Intergenic	19p13.11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4646903	Intergenic	15q24.1	Disease	> 0.01	A CYP1A1 Restriction Fragment Length Polymorphism Is Associated with Breast Cancer in African-American Women
Intergenic	rs4646903	Intergenic	15q24.1	Disease	> 0.01	Genetic polymorphism of estrogen metabolizing enzymes in Siberian women with breast cancer
Intergenic	rs4666451	Intergenic	2p24.1	Protective	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
Intergenic	rs4702131	Intergenic	5p15.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4755816	Intergenic	11p11.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4793090	Intergenic	17q21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4822992	Intergenic	22q12.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs4849887	Intergenic	2q14.2	Disease	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
Intergenic	rs4849887	Intergenic	2q14.2	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs4849887	Intergenic	2q14.2	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs4866496	Intergenic	5p15.33	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs514192	Intergenic	8q22.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs527616	Intergenic	18q11.2	Disease	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
Intergenic	rs527616	Intergenic	18q11.2	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs527616	Intergenic	18q11.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs531874019	Intergenic	20q13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs544173	Intergenic	1p12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs549494279	Intergenic	17q21.31	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs554219	Intergenic	11q13.3	Disease	> 0.01	Functional Variants at the 11q13 Risk Locus for Breast Cancer Regulate Cyclin D1 Expression through Long-Range Enhancers
Intergenic	rs554219	Intergenic	11q13.3	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs559989662	Intergenic	3p21.31	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs56234354	Intergenic	5q35.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs56963355	Intergenic	5p15.33	Protective	> 0.01	Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer
Intergenic	rs58847541	Intergenic	8q24.13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs58847541	Intergenic	8q24.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs59954380	Intergenic	10q23.33	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs59957907	Intergenic	5q11.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs60037937	Intergenic	9q31.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs6012911	Intergenic	20q13.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs6024836	Intergenic	20q13.2	Disease	> 0.01	Genetic Polymorphisms in AURKA and BRCA1 Are Associated With Breast Cancer Susceptibility in a Chinese Han Population
Intergenic	rs60954078	Intergenic	6q25.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs6122906	Intergenic	20q13.13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs614367	Intergenic	11q13.3	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
Intergenic	rs614367	Intergenic	11q13.3	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs62078064	Intergenic	17q12	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs62282635	Intergenic	3q26.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs62355902	Intergenic	5q11.2	Disease	> 0.01	Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1
Intergenic	rs6472903	Intergenic	8q21.11	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs6472903	Intergenic	8q21.11	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs6562760	Intergenic	13q22.1	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs6562760	Intergenic	13q22.1	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Intergenic	rs67397200	Intergenic	19p13.11	Disease	> 0.01	Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
Intergenic	rs67397200	Intergenic	19p13.11	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Intergenic	rs67958007	Intergenic	10p14	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs6796502	Intergenic	3p21.31	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
Intergenic	rs6815814	Intergenic	4p14	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs6890591	Intergenic	5q35.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs6940159	Intergenic	6q27	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7149721	Intergenic	14q11.2	Disease	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
Intergenic	rs72658071	Intergenic	8q21.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs72749841	Intergenic	5q11.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs72749841	Intergenic	5q11.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs72758040	Intergenic	5q11.2	Disease	> 0.01	Heritable genomic diversity in breast cancer driver genes and associations with risk in a Chilean population
Intergenic	rs7297051	Intergenic	12p11.22	Disease	> 0.01	Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
Intergenic	rs7297051	Intergenic	12p11.22	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs7297051	Intergenic	12p11.22	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7304105	Intergenic	12q15	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs733618	Intergenic	2q33.2	Disease	> 0.01	Cytotoxic T-lymphocyte antigen 4 polymorphisms and breast cancer susceptibility: Evidence from a meta-analysis
Intergenic	rs74392007	Intergenic	6q22.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs745570	Intergenic	17q25.3	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
Intergenic	rs7463114	Intergenic	8p12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs74943274	Intergenic	2q33	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs75224640	Intergenic	13q14.2	Disease	< 0.01	Association of breast cancer risk and the mTOR pathway in women of African ancestry in ‘The Root’ Consortium
Intergenic	rs7529522	Intergenic	1p12	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs75772194	Intergenic	8p12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs75915166	Intergenic	11q13.3	Disease	> 0.01	Functional Variants at the 11q13 Risk Locus for Breast Cancer Regulate Cyclin D1 Expression through Long-Range Enhancers
Intergenic	rs75915166	Intergenic	11q13.3	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs763354	Intergenic	6q13	Protective	> 0.01	Genetic Variations in miR-30 Family Member Regulatory Regions Are Associated with Breast Cancer Risk in a Chinese Population
Intergenic	rs76535198	Intergenic	16q22.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7697216	Intergenic	4q34.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7710996	Intergenic	5p12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7716600	Intergenic	5p12	Disease	> 0.01	LncRNA-SNPs in a Brazilian Breast Cancer Cohort: A Case-Control Study
Intergenic	rs77528541	Intergenic	4q28.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs77528541	Intergenic	4q28.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs77554484	Intergenic	15q26.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7799039	Intergenic	7q32.1	Disease	> 0.01	Leptin and leptin receptor polymorphisms are associated with increased risk and poor prognosis of breast carcinoma
Intergenic	rs78540526	Intergenic	11q13.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs7935378	Intergenic	11q22.2	Disease	> 0.01	Common MMP-7 Polymorphisms and Breast Cancer Susceptibility: A Multistage Study of Association and Functionality
Intergenic	rs79858006	Intergenic	18q12.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs8002929	Intergenic	13q22.1	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs8035987	Intergenic	15q24.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs805510	Intergenic	12p11.22	Disease	> 0.01	Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
Intergenic	rs8082452	Intergenic	17q25.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs8176636	Intergenic	9q34.2	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
Intergenic	rs833061	Intergenic	6p21.1	Disease	> 0.01	Association of polymorphisms of angiogenesis genes with breast cancer
Intergenic	rs889312	Intergenic	5q11.2	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
Intergenic	rs889312	Intergenic	5q11.2	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
Intergenic	rs889312	Intergenic	5q11.2	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
Intergenic	rs9257408	Intergenic	6p22.1	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
Intergenic	rs9284657	Intergenic	4q21.23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs9341894	Intergenic	6q14.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs9397437	Intergenic	6q25.1	Disease	> 0.01	Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
Intergenic	rs9420318	Intergenic	10q26.12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs9573140	Intergenic	13q22.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
Intergenic	rs9693444	Intergenic	8p12	Protective	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
Intergenic	rs9693444	Intergenic	8p12	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
Intergenic	rs9712235	Intergenic	2p14	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Intergenic	rs9790879	Intergenic	5p12	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
Intergenic	rs9862599	Intergenic	3q13.11	Disease	> 0.01	Identification of two novel breast cancer loci through large-scale genome-wide association study in the Japanese population
Intergenic	rs9868094	Intergenic	3p24.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
JAK2	rs56118985	Exon	9p24.1	Disease	< 0.01	Identification of Novel Breast Cancer Risk Loci
KANSL1	rs2532263	Intron	17q21.31	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
KCNJ6	rs11910276	Intron	21q22.13	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
KCNJ6	rs2409939	Intron	21q22.13	Protective	> 0.01	Genome‑wide analysis of genetic predisposition to common polygenic cancers
KCNN4	-	-	19q13.31	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
KCNN4	rs56681946	Intron	19q13.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
KIAA1217	rs11014002	Intron	10p12.2	Protective	> 0.01	Association Study of hsa-mir-603 rs11014002 Polymorphism and Risk of Breast Cancer in a Sample of Iranian Population
KLC1	rs1799796	Intron	14q32.33	Protective	> 0.01	Variants in DNA double-strand break repair genes and breast cancer susceptibility
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	Variants in DNA double-strand break repair genes and breast cancer susceptibility
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	Correlation between selected XRCC2, XRCC3 and RAD51 gene polymorphisms and primary breast cancer in women in Pakistan
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	Genetic Variations of DNA Repair Genes in Breast Cancer
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	Relationship between polymorphisms in homologous recombination repair genes RAD51 G172T、XRCC2 & XRCC3 and risk of breast cancer: A meta-analysis
KLC1	rs861539	Intron	14q32.33	Disease	> 0.01	The interplay between XPG-Asp1104His polymorphism and reproductive risk factors elevates risk of breast cancer in Tanzanian women: A multiple interaction analysis
KLC1	rs861539	Intron	14q32.33	Protective	> 0.01	Association of RAD51, XRCC1, XRCC2, and XRCC3 Polymorphisms with Risk of Breast Cancer
KMT2C	rs200662726	Exon	7q36.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
KMT2C	rs772146328	Exon	7q36.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
KRAS	rs9266	3 Prime UTR Variant	12p12.1	Disease	> 0.01	Association between KRAS gene polymorphisms and genetic susceptibility to breast cancer in a Chinese population
L3MBTL3	rs6569648	Intron	6q23.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
L3MBTL3	rs6569648	Intron	6q23.1	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
L3MBTL3	rs6569648	Intron	6q23.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LDLRAD4	rs4797754	Intron	18p11.21	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LEPR	rs1137101	Exon	1p31.3	Disease	> 0.01	Leptin and leptin receptor polymorphisms are associated with increased risk and poor prognosis of breast carcinoma
LEPR	rs1137101	Exon	1p31.3	Disease	> 0.01	Associations among Lipids, Leptin, and Leptin Receptor Gene Gin223Arg Polymorphisms and Breast Cancer in China
LEPR	rs1137101	Exon	1p31.3	Disease	> 0.01	Polymorphic Markers Associated with Genes Responsible for Lipid and Carbohydrate Metabolism Disorders and Insulin Resistance in Cancer Patients
LEPR	rs1137101	Exon	1p31.3	Disease	> 0.01	Effect of leptin receptor Q223R polymorphism on breast cancer risk
LEPR	rs1137101	Exon	1p31.3	Protective	> 0.01	Single-Nucleotide Polymorphisms in LEP and LEPR Associated With Breast Cancer Risk: Results From a Multicenter Case-Control Study in Chinese Females
LEPR	rs1137100	Exon	1p31.3	Protective/Disease	> 0.01	Correlation of Q223R and K109R polymorphisms in leptin receptor gene with susceptibility of breast cancer: A systematic review and meta-analysis
LEPR	rs1137101	Exon	1p31.3	Protective/Disease	> 0.01	Correlation of Q223R and K109R polymorphisms in leptin receptor gene with susceptibility of breast cancer: A systematic review and meta-analysis
LEPR	rs4655555	Intron	1p31.3	Protective	> 0.01	Single-Nucleotide Polymorphisms in LEP and LEPR Associated With Breast Cancer Risk: Results From a Multicenter Case-Control Study in Chinese Females
LGR6	rs17489300	Intron	1q32.1	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
LGR6	rs6678914	Intron	1q32.1	Disease	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
LGR6	rs6678914	Intron	1q32.1	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
LGR6	rs6678914	Intron	1q32.1	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
LGR6	rs12129456	Intron	1q32.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC-PINT	rs2048672	Intron	7q32.3	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
LINC-PINT	rs4593472	Intron	7q32.3	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
LINC-PINT	rs68056147	Intron	7q32.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC00536	rs13267382	Intron	8q23.3	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
LINC00536	rs13267382	Intron	8q23.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC00673	rs11652463	Intron	17q24.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
LINC00673	rs4793442	Intron	17q24.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC00886	rs11281251	Intron	3q25.31	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
LINC00886	rs5853769	Intron	3q25.31	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC01282	rs12689301	Intron	23p11.4	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
LINC01483	rs9302903	Intron	17q24.3	Protective	> 0.01	Common genetic variation and novel loci associated with volumetric mammographic density
LINC01488	rs537626	Non Coding Transcript Variant	11q13.3	Disease	> 0.01	A Genome-wide Association Study of Early-onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age
LINC01612	rs10030422	Intron	4q33	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
LINC02068	rs58058861	Intron	3q26.31	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LINC02288	rs75004998	Intron	14q24.3	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
LINC02288	rs2216310	Intron	14q24.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LINC02456	rs1520220	Intron	12q23.2	Disease	> 0.01	IGF1 and IGFBP3 tagging polymorphisms are associated with circulating levels of IGF1, IGFBP3 and risk of breast cancer
LINC02456	rs855596	Intron	12q23.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LMX1B	rs10760444	Intron	9q33.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LMX1B	rs10760444	Intron	9q33.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC100128494	rs3750913	Non Coding Transcript Variant	11q13.4	Disease	> 0.01	Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility
LOC100287329	rs909253	Intron	6p21.33	Disease	> 0.01	Polymorphisms of tumour necrosis factors A and B in breast cancer
LOC100507346	rs2066829	Non Coding Transcript Variant	9q22.32	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
LOC101927871	rs2151842	Intron	1p22.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC101928278	rs13387042	Intron	2q35	Protective	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
LOC101928278	rs13387042	Intron	2q35	Disease	> 0.01	Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer
LOC101928278	rs13387042	Intron	2q35	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
LOC101928278	rs13387042	Intron	2q35	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
LOC101928278	rs34005590	Intron	2q35	Protective	> 0.01	An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression
LOC101928278	rs4442975	Intron	2q35	Protective	> 0.01	Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation
LOC101929512	rs7309	Intron	2q24.2	Protective	> 0.01	Genetic variation in TLR or NFkappaB pathways and the risk of breast cancer: a case-control study
LOC101929626	rs1707302	Intron	1p34.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC101929626	rs1707302	Intron	1p34.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC102724851	rs71557345	Intron	6p22.2	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC102724851	rs71557345	Non Coding Transcript Variant	6p22.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105369501	rs10891556	Intron	11q23.2	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
LOC105369828	rs61754227	Non Coding Transcript Variant	12q15	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC105369944	rs855596	Intron	12q23.2	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
LOC105370003	rs1292011	Intron	12q24.21	Protective	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
LOC105370003	rs1292011	Intron	12q24.21	Protective	> 0.01	Genome-wide association analysis identifies three new breast cancer susceptibility loci
LOC105370003	rs1292011	Intron	12q24.21	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105371082	rs33989964	Intron	16p13.13	Disease	> 0.01	The importance of SOCS1 - 1478 CA/del polymorphism and expression in breast cancer: a case-control study in the north of Iran
LOC105371274	rs28539243	Intron	16q12.2	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC105371274	rs16953806	Intron	16q12.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105371393	rs4496150	Intron	16q24.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC105373071	rs77848624	Non Coding Transcript Variant	22q13.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105373874	rs13387042	Non Coding Transcript Variant	2q35	Protective	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
LOC105373874	rs13387042	Non Coding Transcript Variant	2q35	Disease	> 0.01	Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer
LOC105373874	rs13387042	Non Coding Transcript Variant	2q35	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
LOC105373874	rs13387042	Non Coding Transcript Variant	2q35	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
LOC105374610	rs17045754	Non Coding Transcript Variant	2p16.2	Protective	> 0.01	Genetic variants in the acylphosphatase 2 gene and the risk of breast cancer in a Han Chinese population
LOC105375404	rs17268829	Intron	7q21.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC105375508	rs972283	Intron	7q32.2	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
LOC105375739	rs17350191	Intron	8q24.13	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
LOC105375739	rs13279803	Intron	8q24.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105376214	rs10816625	Intron	9q31.2	Disease	> 0.01	Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2
LOC105376214	rs13294895	Intron	9q31.2	Disease	> 0.01	Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2
LOC105376214	rs676256	Intron	9q31.2	Protective	> 0.01	Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2
LOC105376214	rs865686	Intron	9q31.2	Protective	> 0.01	Novel Breast Cancer Susceptibility Locus at 9q31.2: Results of a Genome-Wide Association Study
LOC105376214	rs865686	Intron	9q31.2	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
LOC105376214	rs7862747	Intron	9q31.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC105377110	rs2886671	Intron	3p14.2	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
LOC105377110	rs9831300	Intron	3p14.2	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
LOC105377621	rs28362491	Intron	4q24	Disease	> 0.01	Genetic Polymorphisms in Inflammatory Response Genes and Their Associations With Breast Cancer Risk
LOC105377641	rs1375631	Intron	3p24.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
LOC105377871	rs17530068	Intron	6q14.1	Disease	> 0.01	A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11
LOC105379003	rs7727166	Non Coding Transcript Variant	5q12.3	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
LOC107984214	rs7072776	Intron	10p12.31	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
LOC107984270	rs2089176	Intron	10q25.3	Protective	> 0.01	Common genetic variation and novel loci associated with volumetric mammographic density
LOC107984284	rs3813867	Non Coding Transcript Variant	10q26.3	Disease	> 0.01	Association of CYP2E1, STK15 and XRCC1 Polymorphisms with Risk of Breast Cancer in Malaysian Women
LOC107984567	rs2286657	Intron	13q14.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107985393	rs3746444	Intron	20q11.22	Disease	> 0.01	Common Genetic Variants in pre-microRNAs Were Associated With Increased Risk of Breast Cancer in Chinese Women
LOC107985515	rs16992204	Intron	21q22.12	Disease	> 0.01	Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci
LOC107985515	rs12482521	Intron	21q22.12	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107985532	rs384262	Intron	22q11.21	Disease	> 0.01	Association Study of miR-100, miR-124-1, miR-218-2, miR-301b, miR-605, and miR-4293 Polymorphisms and the Risk of Breast Cancer in a Sample of Iranian Population
LOC107985535	rs28512361	Intron	22q13.31	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC107985535	rs77848624	Intron	22q13.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107986528	rs1038304	Intron	6q25.1	Protective	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
LOC107986620	rs7768862	Intron	6q14.3	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
LOC107986620	rs9444166	Intron	6q14.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107986820	rs10953105	Intron	7q21.3	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
LOC107986854	rs11977670	Intron	7q34	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
LOC107986854	rs11977670	Intron	7q34	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107986930	rs144145984	Intron	8p21.2	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
LOC107986930	rs310291	Non Coding Transcript Variant	8p21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC107986961	rs514192	Intron	8q22.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
LOC107987209	rs4983544	Non Coding Transcript Variant	14q32.33	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC112268294	rs1065852	Intron	22q13.2	Disease	> 0.01	Detection of Cytochrome P450 Polymorphisms in Breast Cancer Patients May Impact on Tamoxifen Therapy
LOC124900631	rs4445576	Exon	10q11.22	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124900701	rs12506630	Intron	4q12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC124900868	rs62331150	Intron	4q24	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC124901298	rs369261720	Non Coding Transcript Variant	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124901298	rs372503438	Intron	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124901298	rs41548917	Intron	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124901298	rs41562120	Intron	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124901298	rs758168864	Intron	6p22.1	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
LOC124901435	rs2046210	Non Coding Transcript Variant	6q25.1	Disease	> 0.01	Estrogen receptor alpha (ESR1) gene polymorphism (rs2234693 and rs2046210) with breast cancer risk in pashtun population of Khyber Pakhtunkhwa
LOC124901435	rs2046210	Non Coding Transcript Variant	6q25.1	Disease	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
LOC124902020	rs1121948	Non Coding Transcript Variant	8q24.21	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC124903335	rs10483813	Non Coding Transcript Variant	14q24.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC124905970	rs539902477	Intron	2p25.1	Disease	< 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC124909400	rs35701020	Non Coding Transcript Variant	3q12.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LOC339902	rs9831300	Intron	3p14.2	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
LRTOMT	rs3018301	Intron	11q13.4	Disease	> 0.01	Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility
LRTOMT	rs673478	Intron	11q13.4	Disease	> 0.01	Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility
LSP1	-	-	11p15.5	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
LSP1	rs3817198	Intron	11p15.5	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
LSP1	rs3817198	Intron	11p15.5	Disease	> 0.01	The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis
LSP1	rs4980383	Intron	11p15.5	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
LSP1	rs569550	Intron	11p15.5	Disease	> 0.01	Correlation between LSP1 polymorphisms and the susceptibility to breast cancer
LSP1	rs592373	Intron	11p15.5	Disease	> 0.01	Correlation between LSP1 polymorphisms and the susceptibility to breast cancer
LSP1	rs588321	Intron	11p15.5	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
LTA	rs909253	Intron	6p21.33	Disease	> 0.01	Polymorphisms of tumour necrosis factors A and B in breast cancer
LYPD5	-	-	19q13.31	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
LZTS1	rs903999	Intron	8p21.3	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
MAD1L1	-	CNV	7p22.3	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
MAF	rs1030258012	Exon	16q23.2	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
MAP3K1	-	-	5q11.2	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
MAPK3	rs7698	Non Coding Transcript Variant	16p11.2	Protective	> 0.01	MAPK genes interact with diet and lifestyle factors to alter risk of breast cancer: The Breast Cancer Health Disparities Study
MCC	rs11283943	Intron	5q22.2	Disease	> 0.01	Association of APC and MCC polymorphisms with increased breast cancer risk in an Indian population
MCM8	rs16991615	Exon	20p12.3	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
MCM8	rs16991615	Exon	20p12.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MCPH1	rs747489687	Exon	8p23.1	Disease	< 0.01	Targeted Next-Generation Sequencing Identifies a Recurrent Mutation in MCPH1 Associating With Hereditary Breast Cancer Susceptibility
MCPH1	rs1823375	Intron	8p23.1	Protective	> 0.01	The impact of Angiopoietin-2 genetic polymorphisms on susceptibility for malignant breast neoplasms
MDM2	rs2279744	Intron	12q15	Disease	> 0.01	Significant Association of the MDM2 T309G Polymorphism with Breast Cancer Risk in a Turkish Population
MDM2	rs2279744	Intron	12q15	Disease	> 0.01	Involvement of p53 R72P polymorphism in the association of MDM2-SNP309 with breast cancer
MDM2	rs2279744	Intron	12q15	Disease	> 0.01	Results based on 124 cases of breast cancer and 97 controls from Taiwan suggest that the single nucleotide polymorphism (SNP309) in the MDM2 gene promoter is associated with earlier onset and increased risk of breast cancer
MDM2	rs2279744	Intron	12q15	Disease	> 0.01	A single‐nucleotide polymorphism in the TP53 and MDM‐2 gene modifies breast cancer risk in an ethnic Arab population
MDM2	rs937283	5 Prime UTR Variant	12q15	Disease	> 0.01	The Study of MDM2 rs937283 Variant and Cancer Susceptibility in a Central Chinese Population
MDM4	rs4245739	Non Coding Transcript Variant	1q32.1	Disease	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
MDM4	rs4245739	Non Coding Transcript Variant	1q32.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
MDM4	rs4245739	Non Coding Transcript Variant	1q32.1	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
MDM4	rs2169137	Intron	1q32.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MEAK7	-	CNV	16q24.1	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
MEN1	-	Exon	11q13.1	Disease	< 0.01	Breast-Cancer Predisposition in Multiple Endocrine Neoplasia Type 1
MGA	rs61736074	Exon	15q15	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
MGMT	rs2296675	Intron	10q26.3	Disease	> 0.01	DNA repair gene variants in relation to overall cancer risk: a population-based study
MIER3	-	-	5q11.2	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
MIR149	rs2292832	Non Coding Transcript Variant	2q37.3	Disease	> 0.01	The association between genetic variation rs2292832 and the processing efficiency of pre-mir-149 affects the risk of breast cancer
MIR155HG	rs190708267	Non Coding Transcript Variant	21q21.3	Disease	< 0.01	A Single Variant in Pri-miRNA-155 Associated with Susceptibility to Hereditary Breast Cancer Promotes Aggressiveness in Breast Cancer Cells
MIR196A2	rs11614913	Non Coding Transcript Variant	12q13.13	Disease	> 0.01	Common Genetic Variants in pre-microRNAs Were Associated With Increased Risk of Breast Cancer in Chinese Women
MIR196A2	rs11614913	Non Coding Transcript Variant	12q13.13	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
MIR23AHG	rs1531212	Non Coding Transcript Variant	19p13.12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MIR23AHG	rs895819	Non Coding Transcript Variant	19p13.12	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
MIR27A	rs895819	Non Coding Transcript Variant	19p13.12	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
MIR4713HG	rs10046	Intron	15q21.2	Disease	> 0.01	Analysis of CYP17, CYP19 and CYP1A1 Gene Polymorphisms in Iranian Women With Breast Cancer
MIR4713HG	rs1008805	Intron	15q21.2	Disease	> 0.01	A CYP19 (aromatase) polymorphism is associated with increased premenopausal breast cancer risk
MIR499A	rs3746444	Non Coding Transcript Variant	20q11.22	Disease	> 0.01	Common Genetic Variants in pre-microRNAs Were Associated With Increased Risk of Breast Cancer in Chinese Women
MIR499B	rs3746444	Non Coding Transcript Variant	20q11.22	Disease	> 0.01	Common Genetic Variants in pre-microRNAs Were Associated With Increased Risk of Breast Cancer in Chinese Women
MIR520F	rs75598818	Non Coding Transcript Variant	19q13.42	Protective	> 0.01	Association of a Potential Functional mir-520f rs75598818 G>A Polymorphism With Breast Cancer
MIR603	rs11014002	Non Coding Transcript Variant	10p12.2	Protective	> 0.01	Association Study of hsa-mir-603 rs11014002 Polymorphism and Risk of Breast Cancer in a Sample of Iranian Population
MIR608	rs4919510	Non Coding Transcript Variant	10q24.31	Protective	> 0.01	miR-608 rs4919510 C>G Polymorphism Decreased the Risk of Breast Cancer in an Iranian Subpopulation
MLH1	rs1799977	Exon	3p22.2	Protective	> 0.01	Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk
MLH3	rs175080	Exon	14q24.3	Protective	> 0.01	Association of common variants in mismatch repair genes and breast cancer susceptibility: a multigene study
MLLT10	rs1243182	Intron	10p12.31	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
MLLT10	rs7098100	Intron	10p12.31	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MLLT1	rs11880101	Exon	19p13.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
MMP1	rs5854	3 Prime UTR Variant	11q22.2	Protective	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP1	rs7125062	Intron	11q22.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP1	rs996999	Intron	11q22.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP2	rs11541998	Exon	16q12.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP2	rs243845	Intron	16q12.2	Protective	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP3	rs650108	Intron	11q22.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MMP9	rs17576	Exon	20q13.12	Disease	> 0.01	Genetic variation in TLR or NFkappaB pathways and the risk of breast cancer: a case-control study
MMP9	rs17576	Exon	20q13.12	Protective	> 0.01	Matrix Metalloproteinase Gene Polymorphisms Are Associated with Breast Cancer in the Caucasian Women of Russia
MMP9	rs2250889	Exon	20q13.12	Protective	> 0.01	Matrix Metalloproteinase Gene Polymorphisms Are Associated with Breast Cancer in the Caucasian Women of Russia
MMP9	rs3787268	Intron	20q13.12	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
MRE11	-	Exon	11q21	Disease	< 0.01	Rare key functional domain missense substitutions in MRE11A, RAD50, and NBN contribute to breast cancer susceptibility: results from a Breast Cancer Family Registry case-control mutation-screening study
MRPL23	rs2107425	Intron	11p15.5	Protective	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
MRPL23	rs217727	Intron	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
MRPL23	rs2839698	Intron	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
MRPL23	rs3741219	Intron	11p15.5	Disease	> 0.01	Association between long non-coding RNA H19 polymorphisms and breast cancer risk: a meta-analysis
MRPS18C	rs11099601	3 Prime UTR Variant	4q21.23	Disease	> 0.01	Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21
MRTFA	rs6001930	Intron	22q13.1	Disease	> 0.01	Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer
MRTFA	rs6001930	Intron	22q13.1	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
MRTFA	rs1246457062	Intron	22q13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MSH2	-	Exon	2p21-p16.3	Disease	< 0.01	Association between the Lynch syndrome gene MSH2 and breast cancer susceptibility in a Canadian familial cancer registry
MSH6	-	Exon	2p16.3	Disease	< 0.01	MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer
MSH6	-	Exon	2p16.3	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
MSH6	-	Exon	2p16.3	Protective	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
MSTO1	rs12091730	Intron	1q22	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MTCL1	rs2111836	Intron	18p11.2	Disease	> 0.01	A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia
MTCL1	rs8087976	Intron	18p11.2	Disease	> 0.01	A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Association of MTHFR, MTRR and MTR polymorphisms with breast cancer risk: a study in Chinese females
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Methylenetetrahydrofolate reductase polymorphism and susceptibility to breast cancer
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	One-Carbon Metabolism, MTHFR Polymorphisms, and Risk of Breast Cancer
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Methylenetetrahydrofolate Reductase C677T polymorphism and breast cancer risk in Moroccan women
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Association between dietary intake of folate and MTHFR and MTR genotype with risk of breast cancer
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Evaluation of the Contribution of Methylenetetrahydrofolate Reductase Genotypes to Taiwan Breast Cancer
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Association of methylenetetrahydrofolate reductase and methionine synthase polymorphisms with breast cancer risk and interaction with folate, vitamin B6, and vitamin B 12 intakes
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Polymorphisms in the MTHFR gene are associated with breast cancer risk and prognosis in a Chinese population
MTHFR	rs1801133	Exon	1p36.22	Disease	> 0.01	Association of MTHFR 677C>T polymorphism with breast cancer risk: A case-control study and meta-analysis
MTMR11	rs11205303	Exon	1q21.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
MTR	rs1050993	3 Prime UTR Variant	1q43	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
MTR	rs1770449	Intron	1q43	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
MTR	rs1805087	Exon	1q43	Protective	> 0.01	Role of polymorphism of methyltetrahydrofolate-homocysteine methyltransferase (MTR) A2756G and breast cancer risk
MTR	rs1805087	Exon	1q43	Protective	> 0.01	Genetic polymorphisms in the one‐carbon metabolism pathway and breast cancer risk: A population‐based case–control study and meta‐analyses
MTR	rs1805087	Exon	1q43	Disease	> 0.01	Associations of polymorphisms of folate cycle enzymes and risk of breast cancer in a Brazilian population are age dependent
MTRR	rs162049	Intron	5p15.31	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
MTRR	rs1801394	Exon	5p15.31	Disease	> 0.01	Association of MTHFR, MTRR and MTR polymorphisms with breast cancer risk: a study in Chinese females
MUC4	rs868560707	Exon	3q29	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
MUS81	rs61754785	Exon	11q13.1	Disease	> 0.01	Germline Mutation in MUS81 Resulting in Impaired Protein Stability is Associated with Familial Breast and Thyroid Cancer
MUTYH	-	Exon	1p34.1	Disease	< 0.01	Multiplicity in polyp count and extracolonic manifestations in 40 Dutch patients with MYH associated polyposis coli (MAP)
MUTYH	-	Exon	1p34.1	Disease	< 0.01	Expanded Extracolonic Tumor Spectrum in MUTYH -Associated Polyposis
MUTYH	rs34612342	Exon	1p34.1	Disease	< 0.01	Contribution of MUTYH Variants to Male Breast Cancer Risk: Results From a Multicenter Study in Italy
MUTYH	rs36053993	Exon	1p34.1	Disease	< 0.01	MutYH mutation carriers have increased breast cancer risk
MYC	rs4645959	Exon	8q24.21	Disease	> 0.01	c-MYC Asn11Ser is associated with increased risk for familial breast cancer
MYH7B	rs3746444	Intron	20q11.22	Disease	> 0.01	Common Genetic Variants in pre-microRNAs Were Associated With Increased Risk of Breast Cancer in Chinese Women
MYO5A	rs61731219	Exon	15q21.2	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
NAT2	rs1799930	Exon	8p22	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
NBEA	-	Exon	13q13.3	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
NBN	rs1187082186	Exon	8q21.3	Disease	< 0.01	Germline 657del5 mutation in the NBS1 gene in breast cancer patients
NBN	rs1187082186	Exon	8q21.3	Disease	< 0.01	Germline Mutations 657del5 of the NBS1 Gene Contribute Significantly to the Incidence of Breast Cancer in Central Poland
NCOA1	rs200648189	Intron	2p23.3	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
NCOA3	rs2076546	Exon	20q13.12	Protective	> 0.01	Association of NCOA3 Polymorphisms with Breast Cancer Risk
NCOA3	rs2230782	Exon	20q13.12	Protective	> 0.01	Association of NCOA3 Polymorphisms with Breast Cancer Risk
NDUFB3	rs116739540	Intron	2q33.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
NEK10	rs552647	Intron	3p24.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
NF1	-	Exon	17q11.2	Disease	< 0.01	Increased risk of breast cancer in women with NF1
NF1	-	Exon	17q11.2	Disease	< 0.01	Age-specific risk of breast cancer in women with neurofibromatosis type 1
NF1	-	Exon	17q11.2	Disease	< 0.01	A prospective study of neurofibromatosis type 1 cancer incidence in the UK
NF1	-	Exon	17q11.2	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
NF1	-	Exon	17q11.2	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
NFIA	rs12727993	Intron	1p31.3	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
NFIX	rs78269692	Intron	19p13.13	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
NFIX	rs78269692	Intron	19p13.13	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
NLGN4X	-	CNV	Xp22.31	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
NOS3	rs1799983	Exon	7q36.1	Disease	> 0.01	Polymorphisms of the endothelial nitric oxide synthase gene in breast cancer
NOTCH3	rs200504060	Exon	19p13.12	Disease	< 0.01	Identification of Novel Breast Cancer Risk Loci
NPHP1	-	CNV	2q13	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
NQO1	rs1800566	Exon	16q22.1	Disease	> 0.01	Breast cancer: role of polymorphisms in biotransformation enzymes
NQO2	rs2071002	5 Prime UTR Variant	6p25.2	Protective	> 0.01	Functional polymorphisms, altered gene expression and genetic association link NRH:quinone oxidoreductase 2 to breast cancer with wild-type p53
NR2F6	rs891205	Intron	19p13.12	Disease	> 0.01	Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
NREP	rs6882649	Intron	5q22.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
NREP	rs6594555	Intron	5q22.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
NRG1	rs113317778	Exon	8p12	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
NTRK1	rs6336	Exon	1q23.1	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
NTRK1	rs6339	Exon	1q23.1	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
NUMA1	rs3750913	Exon	11q13.4	Disease	> 0.01	Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility
NUP214	rs61756081	Exon	9q34.13	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
OGG1	rs1052133	Exon	3p25.3	Disease	> 0.01	Genetic polymorphism of hOGG1 ser326cys and its association with breast cancer in Jammu and Kashmir
OGG1	rs1052133	Exon	3p25.3	Disease	> 0.01	The hOGG1 Ser326Cys Gene Polymorphism and Breast Cancer Risk in Saudi Population
OR2A1-AS1	rs62485509	Intron	7q35	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
OR4C11	-	CNV	11q11	Disease	-	Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry
OR4P4	-	CNV	11q11	Disease	-	Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry
ORC2	rs17383256	Intron	2q33.1	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
OTUD7B	rs12048493	Intron	1q21.2	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
P3R3URF-PIK3R3	rs1707302	Intron	1p34.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
P3R3URF-PIK3R3	rs1707302	Intron	1p34.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PALB2	-	Exon	16p12.2	Disease	< 0.01	PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene
PALB2	-	Exon	16p12.2	Disease	< 0.01	Breast-Cancer Risk in Families with Mutations in PALB2
PALB2	-	Exon	16p12.2	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
PALB2	-	Exon	16p12.2	Disease	< 0.01	Male breast cancer risk associated with pathogenic variants in genes other than BRCA1/2: an Italian case-control study
PALB2	-	Exon	16p12.2	Disease	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
PALB2	-	Exon	16p12.2	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
PALB2	rs180177102	Exon	16p12.2	Disease	< 0.01	A Recurrent Mutation in PALB2 in Finnish Cancer Families
PARP1	rs1136410	Exon	1q42.12	Protective	> 0.01	Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk
PAX9	rs2236007	Intron	14q13.3	Protective	> 0.01	Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls
PAX9	rs2236007	Intron	14q13.3	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
PAX9	rs12881240	Exon	14q13.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PCDHGB2	-	CNV	5q31	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
PCM1	rs1302934371	Intron	8p22	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PCNT	rs35418111	Intron	21q22.3	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
PCNT	rs9808759	Intron	21q22.3	Disease	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
PCNT	rs35418111	Intron	21q22.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PCSK7	rs36028244	Intron	11q23.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PDCD6-AHRR	rs62641919	Intron	5p15.33	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PDCD6-AHRR	rs62641919	Intron	5p15.33	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PDE4D	rs1353747	Intron	5q11.2	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
PDE7B	rs11154838	Intron	6q23.3	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
PDGFRB	rs41287110	Exon	5q32	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
PEX14	rs10864459	Intron	1p36.22	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
PEX14	rs616488	Intron	1p36.22	Protective	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
PEX14	rs616488	Intron	1p36.22	Protective	> 0.01	Genome-wide association studies identify four ER negative–specific breast cancer risk loci
PEX14	rs2506885	Intron	1p36.22	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PEX14	rs616488	Intron	1p36.22	Disease	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
PGR	rs1042838	Exon	11q22.1	Disease	> 0.01	Commonly Studied Single-Nucleotide Polymorphisms and Breast Cancer: Results From the Breast Cancer Association Consortium
PHF20	rs112208395	Intron	20q11.22	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PHLDA3	rs35383942	Exon	1q32.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PHLDA3	rs35383942	Exon	1q32.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PIDD1	rs6597981	Intron	11p15.5	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PIDD1	rs6597981	Intron	11p15.5	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PIK3CA	rs121913281	Exon	3q26.32	Disease	> 0.01	Potential Impact of PI3K-AKT Signaling Pathway Genes, KLF-14, MDM4, miRNAs 27a, miRNA-196a Genetic Alterations in the Predisposition and Progression of Breast Cancer Patients
PIK3R3	rs1707302	Intron	1p34.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PIK3R3	rs1707302	Intron	1p34.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PIP4K2A	rs541079479	Intron	10p12.2	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
PIP4K2A	rs541079479	Intron	10p12.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PLA2G6	rs738321	Intron	22q13.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PLA2G6	rs738323	Intron	22q13.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PMF1	rs2758598	Intron	1q22	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
PMF1-BGLAP	rs2758598	Intron	1q22	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
PMS2	-	Exon	7p22.1	Disease	< 0.01	MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer
PMS2P5	rs111422494	Intron	7q11.23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PNPLA4	-	CNV	Xp22.31	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
POGLUT3	rs11374964	3 Prime UTR Variant	11q22.3	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
POGLUT3	rs74911261	Exon	11q22.3	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
POLG	rs145289229	Exon	15q26.1	Disease	< 0.01	Rare missense mutations in RECQL and POLG associate with inherited predisposition to breast cancer
POLR3C	rs143384623	Intron	1q21.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PON1	rs854560	Exon	7q21.3	Disease	> 0.01	Association of Polymorphisms in the Paraoxonase 1 Gene with Breast Cancer Incidence in the CPS-II Nutrition Cohort
PON1	rs854560	Exon	7q21.3	Disease	> 0.01	CYP17, GSTP1, PON1 and GLO1 gene polymorphisms as risk factors for breast cancer: an Italian case-control study
PON1	rs854560	Exon	7q21.3	Disease	> 0.01	Genetic Polymorphisms of Paraoxonase 1 (PON1) Gene: Association Between L55M or Q192R with Breast Cancer Risk and Clinico-Pathological Parameters
PON1	rs854560	Exon	7q21.3	Disease	> 0.01	Association of L55M and Q192R Polymorphisms in Paraoxonase 1 (PON1) Gene With Breast Cancer Risk and Their Clinical Significance
PON1	rs854560	Exon	7q21.3	Disease	> 0.01	A common genetic variation in paraoxonase 1 and risk of breast cancer: a literature review, meta-analysis, and in silico analysis
POR	rs10262966	Exon	7q11.23	Disease	> 0.01	A Variant in the Cytochrome p450 Oxidoreductase Gene Is Associated With Breast Cancer Risk in African Americans
PPA2	rs77928427	Intron	4q24	Disease	> 0.01	Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk
PPARA	rs1800206	Exon	22q13.31	Disease	> 0.01	Impact of Interaction Between PPAR Alpha and PPAR Gamma on Breast Cancer Risk in the Chinese Han Population
PPARA	rs4253760	Intron	22q13.31	Disease	> 0.01	Peroxisome proliferator-activated receptor-alpha (PPARA) genetic polymorphisms and breast cancer risk: a Long Island ancillary study
PPARG	rs1805192	Exon	3p25.2	Disease	> 0.01	Impact of Interaction Between PPAR Alpha and PPAR Gamma on Breast Cancer Risk in the Chinese Han Population
PPARGC1A	rs3736265	Exon	4p15.2	Disease	> 0.01	Associations of genetic variants in the estrogen receptor coactivators PPARGC1A, PPARGC1B and EP300 with familial breast cancer
PPARGC1B	rs7732671	Exon	5q32	Disease	> 0.01	Associations of genetic variants in the estrogen receptor coactivators PPARGC1A, PPARGC1B and EP300 with familial breast cancer
PPIL3	rs115635831	Intron	2q33	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
PPM1D	-	Exon	17q23.2	Disease	< 0.01	Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer
PPM1K-DT	rs10022462	Intron	4q22.1	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
PPM1K-DT	rs10022462	Intron	4q22.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PPP3CA	rs17030831	Intron	4q23	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
PRC1	rs2290203	Intron	15q26.1	Disease	> 0.01	Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1
PRC1	rs8042680	Intron	15q26.1	Protective	> 0.01	Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry
PRC1-AS1	rs2290203	Intron	15q26.1	Disease	> 0.01	Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1
PRC1-AS1	rs8042680	Intron	15q26.1	Protective	> 0.01	Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry
PRDM2	rs2235515	Intron	1p36.21	Disease	> 0.01	Genetic variants in epigenetic genes and breast cancer risk
PRKG1	rs1937680	Intron	10q11.23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
PSMG4	rs9391988	3 Prime UTR Variant	6p25.2	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
PTCH1	rs2066829	Intron	9q22.32	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH1	rs2236405	Exon	9q22.32	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH1	rs2277184	Intron	9q22.32	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH1	rs357564	Exon	9q22.32	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH2	rs11211040	Intron	1p34.1	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH2	rs11573590	Exon	1p34.1	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTCH2	rs3795720	Intron	1p34.1	Protective	> 0.01	Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers
PTEN	-	Exon	10q23.31	Disease	< 0.01	Inherited Mutations in PTEN That Are Associated with Breast Cancer, Cowden Disease, and Juvenile Polyposis
PTEN	-	Exon	10q23.31	Disease	< 0.01	High cumulative risks of cancer in patients with PTEN hamartoma tumour syndrome
PTEN	-	Exon	10q23.31	Disease	< 0.01	Lifetime Cancer Risks in Individuals with Germline PTEN Mutations
PTEN	-	Exon	10q23.31	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
PTEN	-	Exon	10q23.31	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
PTGS1	rs10306194	3 Prime UTR Variant	9q33.2	Disease	> 0.01	Associations between ALOX, COX, and CRP polymorphisms and breast cancer among Hispanic and non‐Hispanic white women: The breast cancer health disparities study
PTPN9	rs8027365	Intron	15q24.2	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
PTPRB	rs61754227	Exon	12q15	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RABEP1	rs61735455	Exon	17p13.2	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RAD50	rs751781524	Exon	5q31.1	Disease	< 0.01	RAD50 and NBS1 are breast cancer susceptibility genes associated with genomic instability
RAD51	rs1801320	Intron	15q15.1	Disease	> 0.01	Correlation between selected XRCC2, XRCC3 and RAD51 gene polymorphisms and primary breast cancer in women in Pakistan
RAD51B	-	Exon	14q24.1	Disease	< 0.01	Germline RAD51B variants confer susceptibility to breast and ovarian cancers deficient in homologous recombination
RAD51B	rs10483813	Intron	14q24.1	Protective	> 0.01	Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium
RAD51B	rs1314913	Intron	14q24.1	Disease	> 0.01	RAD51B in Familial Breast Cancer
RAD51B	rs2588809	Intron	14q24.1	Disease	> 0.01	RAD51B in Familial Breast Cancer
RAD51B	rs2588809	Intron	14q24.1	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
RAD51B	rs2588809	Intron	14q24.1	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
RAD51B	rs8009944	Intron	14q24.1	Protective	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
RAD51B	rs999737	Intron	14q24.1	Protective	> 0.01	Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium
RAD51B	rs999737	Intron	14q24.1	Disease	> 0.01	RAD51B in Familial Breast Cancer
RAD51B	rs999737	Intron	14q24.1	Protective	> 0.01	A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
RAD51B	rs10483813	Intron	14q24.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
RAD51B	rs1744947	Intron	14q24.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
RAD51C	-	Exon	17q22	Disease	< 0.01	Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene
RAD51C	-	Exon	17q22	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
RAD51C	-	Exon	17q22	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
RAD51D	-	Exon	17q12	Disease	< 0.01	Triple-Negative Breast Cancer Risk Genes Identified by Multigene Hereditary Cancer Panel Testing
RAD51D	-	Exon	17q12	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
RAD51D	-	Exon	17q12	Disease	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
RAD51D	-	Exon	17q12	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
RAD51D	rs28363284	Exon	17q12	Disease	< 0.01	The variant E233G of the RAD51D gene could be a low‐penetrance allele in high‐risk breast cancer families without BRCA1/2 mutations
RAD51D	rs753862052	Exon	17q12	Disease	< 0.01	Associations between RAD51D germline mutations and breast cancer risk and survival in BRCA1/2-negative breast cancers
RAD51L3-RFFL	rs28363284	Non Coding Transcript Variant	17q12	Disease	< 0.01	The variant E233G of the RAD51D gene could be a low‐penetrance allele in high‐risk breast cancer families without BRCA1/2 mutations
RAD51L3-RFFL	rs753862052	Intron	17q12	Disease	< 0.01	Associations between RAD51D germline mutations and breast cancer risk and survival in BRCA1/2-negative breast cancers
RAD51	rs1801320	Intron	15q15.1	Disease	> 0.01	Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women
RAD51	rs1801320	Intron	15q15.1	Protective	> 0.01	Association of RAD51, XRCC1, XRCC2, and XRCC3 Polymorphisms with Risk of Breast Cancer
RAD51	rs1801321	Intron	15q15.1	Disease	> 0.01	Relationship between polymorphisms in homologous recombination repair genes RAD51 G172T、XRCC2 & XRCC3 and risk of breast cancer: A meta-analysis
RAD52	-	CNV deletion	12p13.33	Disease	< 0.01	Exome sequencing identified rare recurrent copy number variants and hereditary breast cancer susceptibility
RALY	rs2284378	Intron	20q11	Disease	> 0.01	A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11
RALY	rs2284378	Intron	20q11.21	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
RASSF1	rs2073498	Exon	3p21.31	Protective	> 0.01	Exome sequencing identifies RASSF1 and KLK3 germline variants in an Iranian multiple-case breast cancer family
RBBP8	rs1467584861	Exon	18q11.2	Disease	< 0.01	Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability
RBFOX1	rs17823421	Intron	16p13.3	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
RCC2	rs6586541	Intron	1p36.13	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
RECQL	-	Exon	12p12.1	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
RECQL	rs376839517	Exon	12p12.1	Disease	< 0.01	Germline RECQL mutations are associated with breast cancer susceptibility
RECQL	rs777214281	Exon	12p12.1	Disease	< 0.01	Rare missense mutations in RECQL and POLG associate with inherited predisposition to breast cancer
RECQL5	-	Exon	17q25	Disease	-	A Large Case-Control Study Performed in Spanish Population Suggests That RECQL5 Is the Only RECQ Helicase Involved in Breast Cancer Susceptibility
RIN3	rs11627032	Intron	14q32.12	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
RIN3	rs78440108	Intron	14q32.12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
RINT1	rs143184349	Exon	7q22.3	Disease	< 0.01	Rare mutations in RINT1 predispose carriers to breast and Lynch Syndrome-spectrum cancers
RINT1	rs150793856	Exon	7q22.3	Disease	< 0.01	Rare mutations in RINT1 predispose carriers to breast and Lynch Syndrome-spectrum cancers
RNF115	rs12405132	Intron	1q21.1	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
RNF146	rs2180341	Intron	6q22.33	Disease	> 0.01	Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
RNF146	rs6569479	Intron	6q22.33	Disease	> 0.01	Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
RNF19A	rs2849506	Intron	8q22.2	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
RNF19A	rs2849506	Intron	8q22.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
RNF213	rs62077764	Exon	17q25.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF213-AS1	rs61745599	Intron	17q25.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF213-AS1	rs62077764	Intron	17q25.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF213	rs61745599	Exon	17q25.3	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF43	rs142097313	Exon	17q22	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF43	rs2680701	Exon	17q22	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RNF43	rs34523089	Exon	17q22	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
ROPN1L	rs1092913	Intron	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
ROS1	rs2229079	Exon	6q22.1	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
RP11.363G10.2	-	CNV	Xp11.22	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
RPL23AP53	rs66823261	Intron	8p23.3	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
RPS6KA2	-	CNV	6q27	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
RPS6KA3	rs114874970	Intron	Xp22.12	Disease	> 0.01	Association of breast cancer risk and the mTOR pathway in women of African ancestry in ‘The Root’ Consortium
RSU1	-	CNV	10p13	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
SCFD2	rs11947923	Intron	4q12	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
SCFD2	rs12506630	Intron	4q12	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SDC4	rs1981429	Intron	20q13.12	Disease	> 0.01	SDC4-rs1981429 and ATM-rs228590 may provide early biomarkers of breast cancer risk
SELENOP	rs3877899	Exon	5p12	Protective	> 0.01	Association between Polymorphisms in Glutathione Peroxidase and Selenoprotein P Genes, Glutathione Peroxidase Activity, HRT Use and Breast Cancer Risk
SEMA4G	rs4919510	Intron	10q24.31	Protective	> 0.01	miR-608 rs4919510 C>G Polymorphism Decreased the Risk of Breast Cancer in an Iranian Subpopulation
SERPINA3	rs199710314	Splice Acceptor Variant	14q32.13	Disease	< 0.01	Exome sequencing identifies a recurrent variant in SERPINA3 associating with hereditary susceptibility to breast cancer
SETBP1	rs11875595	Intron	18q12.3	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
SETBP1	rs6507583	Intron	18q12.3	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
SETBP1	rs6507583	Intron	18q12.3	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
SETBP1	rs9954058	Intron	18q12.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SHBG	rs6257	Intron	17p13.1	Protective	> 0.01	Identification of common variants in the SHBG gene affecting sex hormone-binding globulin levels and breast cancer risk in postmenopausal women
SHC1	rs8191979	Exon	1q21.3	Protective	> 0.01	The insulin-like growth factor-1 pathway mediator genes: SHC1 Met300Val shows a protective effect in breast cancer
SHMT1	rs1979277	Exon	17p11.2	Disease	> 0.01	Associations of polymorphisms of folate cycle enzymes and risk of breast cancer in a Brazilian population are age dependent
SHMT1	rs1979277	Exon	17p11.2	Protective	> 0.01	Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan
SIAH2	rs60538652	Intron	3q25.1	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
SIAH2	rs6788895	Intron	3q25.1	Disease	> 0.01	A genome-wide association study identifies a genetic variant in the SIAH2 locus associated with hormonal receptor-positive breast cancer in Japanese
SIAH2	rs73006998	Intron	3q25.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SIPA1	rs3741378	Exon	11q13.1	Disease	> 0.01	The Relationship between the Mutation rs3741378 of SIPA1 Gene and Breast Cancer in Vietnamese Women
SIRT3	-	Intron	11p15.5	Disease	-	VNTR Polymorphism in the Intron 5 of SIRT3 and Susceptibility to Breast Cancer
SLC12A5-AS1	rs2250889	Non Coding Transcript Variant	20q13.12	Protective	> 0.01	Matrix Metalloproteinase Gene Polymorphisms Are Associated with Breast Cancer in the Caucasian Women of Russia
SLC14A2	rs17743054	Intron	18q12.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
SLC14A2	rs9952980	Intron	18q12.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SLC19A1	rs1051266	Exon	4p14	Protective	> 0.01	Associations of polymorphisms of folate cycle enzymes and risk of breast cancer in a Brazilian population are age dependent
SLC22A23	rs9391988	Intron	6p25.2	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
SLC36A4	rs1508608	Intron	11q21	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
SLC39A11	rs4969001	Intron	17q25.1	Disease	> 0.01	BRCA1/2-negative, high-risk breast cancers (BRCAX) for Asian women: genetic susceptibility loci and their potential impacts
SLC4A7	rs4973768	Non Coding Transcript Variant	3p24.1	Disease	> 0.01	Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2
SLC4A7	rs4973768	Non Coding Transcript Variant	3p24.1	Disease	> 0.01	The SLC4A7 variant rs4973768 is associated with breast cancer risk: evidence from a case-control study and a meta-analysis
SLC4A7	rs4973768	Non Coding Transcript Variant	3p24.1	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
SLC4A7	rs4973768	Non Coding Transcript Variant	3p24.1	Disease	> 0.01	Update on the relationship between the SLC4A7 variant rs4973768 and breast cancer risk: a systematic review and meta-analysis
SLC6A4	rs140701	Intron	17q11.2	Disease	> 0.01	Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women
SLC8A1	rs727477	Intron	2p22.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SLIT3	rs11134527	Intron	5q35.1	Disease	> 0.01	Association Study of miR-100, miR-124-1, miR-218-2, miR-301b, miR-605, and miR-4293 Polymorphisms and the Risk of Breast Cancer in a Sample of Iranian Population
SMARCA2	-	Exon	9p24.3	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
SMC2	rs10820600	Non Coding Transcript Variant	9q31.1	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
SMC2	rs4742903	Intron	9q31.1	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
SMC2	rs10820600	Intron	9q31.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SNX32	rs548082010	Intron	11q13.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SOD1	rs1041740	Intron	21q22.11	Disease	> 0.01	SOD1 gene variants rs4817415, rs2070424, and rs1041740 and their association with breast cancer risk
SOD1	rs2070424	Intron	21q22.11	Disease	> 0.01	SOD1 gene variants rs4817415, rs2070424, and rs1041740 and their association with breast cancer risk
SOD2	rs4880	Exon	6q25.3	Protective	> 0.01	Oxidative stress-related enzyme gene polymorphisms and susceptibility to breast cancer in non-smoking, non-alcohol-consuming Taiwanese women: a case-control study
SOD2	rs5746136	Intron	6q25.3	Protective	> 0.01	Association of SOD2 rs2758339, rs5746136 and rs2842980 polymorphisms with increased risk of breast cancer: a haplotype-based case-control study
SPDYE12	rs111422494	Intron	7q11.23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SRD5A2	rs523349	Exon	2p23.1	Disease	> 0.01	SRD5A2 gene polymorphisms affect the risk of breast cancer
SRGAP2C	-	-	1p11.2	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
SSBP2	rs6887937	Intron	5q14.1	Disease	> 0.01	A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia
SST	rs4988513	Intron	3q27.3	Protective	> 0.01	Polymorphisms in genes involved in GH1 release and their association with breast cancer risk
SST	rs4988513	Intron	3q27.3	Disease	> 0.01	Genetic Variation in the Growth Hormone Synthesis Pathway in Relation to Circulating Insulin-Like Growth Factor-I, Insulin-Like Growth Factor Binding Protein-3, and Breast Cancer Risk: Results from the European Prospective Investigation into Cancer and Nutrition Study
SSTR2	rs1466113	Intron	17q25.1	Protective	> 0.01	Genetic Variation in the Growth Hormone Synthesis Pathway in Relation to Circulating Insulin-Like Growth Factor-I, Insulin-Like Growth Factor Binding Protein-3, and Breast Cancer Risk: Results from the European Prospective Investigation into Cancer and Nutrition Study
STAU2	rs6991116	Intron	8q21.11	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
STK11	-	Exon	19p13.3	Disease	< 0.01	Frequency and Spectrum of Cancers in the Peutz-Jeghers Syndrome
STRADB	rs16837635	Intron	2q33.1	Disease	> 0.01	Association of breast cancer risk and the mTOR pathway in women of African ancestry in ‘The Root’ Consortium
STT3A-AS1	rs2155388	Intron	3q23	Disease	> 0.01	Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer
STXBP4	rs1156287	Exon	17q22	Protective	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
STXBP4	rs2787486	Intron	17q22	Protective	> 0.01	Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)
STXBP4	rs6504950	Intron	17q22	Protective	> 0.01	Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2
STXBP4	rs244373	Intron	17q22	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
SUB1	rs2012709	Intron	5p13.3	Disease	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
SULT1A1	rs1042028	Exon	16p11.2	Disease	> 0.01	Sulfotransferase 1A1 Polymorphism, Endogenous Estrogen Exposure, Well-done Meat Intake, and Breast Cancer Risk
SULT1A1	rs1042028	Exon	16p11.2	Disease	> 0.01	CYP17 and SULT1A1 Gene Polymorphisms in Indian Breast Cancer
SULT1A1	rs1042028	Exon	16p11.2	Disease	> 0.01	Genetic polymorphism of estrogen metabolizing enzymes in Siberian women with breast cancer
SULT1E1	rs3775778	Intron	4q13.3	Protective	> 0.01	Genetic polymorphisms of SULT1A1 and SULT1E1 and the risk and survival of breast cancer
SUPT3H	-	CNV	6p21.1	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
TAB2	rs9485372	Intron	6q25.1	Protective	> 0.01	Genome-Wide Association Study in East Asians Identifies Novel Susceptibility Loci for Breast Cancer
TAB2	rs574009266	Intron	6q25.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TANK	rs7309	3 Prime UTR Variant	2q24.2	Protective	> 0.01	Genetic variation in TLR or NFkappaB pathways and the risk of breast cancer: a case-control study
TBX1	rs34331122	Intron	22q11.21	Protective	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
TBX1	rs34331122	Intron	22q11.21	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TBX3	rs1061657	3 Prime UTR Variant	12q24.21	Disease	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
TBX3	rs12366395	5 Prime UTR Variant	12q24.21	Disease	> 0.01	Heritable genomic diversity in breast cancer driver genes and associations with risk in a Chilean population
TCF7L2	rs12255372	Intron	10q25.2	Disease	> 0.01	Transcription Factor 7-like 2 (TCF7L2) Variant Is Associated With Familial Breast Cancer Risk: A Case-Control Study
TCF7L2	rs12255372	Intron	10q25.2	Protective	> 0.01	Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes With Breast Cancer in Saudi Patients
TCF7L2	rs12255372	Intron	10q25.2	Disease	> 0.01	Genotypes and Haplotypes in the AXIN2 and TCF7L2 Genes are Associated With Susceptibility and With Clinicopathological Characteristics in Breast Cancer Patients
TCF7L2	rs6585202	Intron	10q25.2	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
TCF7L2	rs7903146	Intron	10q25.2	Disease	> 0.01	Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry
TCF7L2	rs7903146	Intron	10q25.2	Disease	> 0.01	Genotypes and Haplotypes in the AXIN2 and TCF7L2 Genes are Associated With Susceptibility and With Clinicopathological Characteristics in Breast Cancer Patients
TCF7L2	rs7904519	Intron	10q25.2	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
TEC	rs11944638	Intron	4p11	Disease	> 0.01	Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
TEC	rs11944638	Intron	4p11	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TEFM	rs10612648	Intron	17q11.2	Protective	> 0.01	Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
TERT	rs10069690	Intron	5p15.33	Disease	> 0.01	A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer
TERT	rs10069690	Intron	5p15.33	Disease	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
TERT	rs10069690	Intron	5p15.33	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
TERT	rs2242652	Intron	5p15.33	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
TERT	rs7726159	Intron	5p15.33	Disease	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
TERT	rs7726159	Intron	5p15.33	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
TERT	rs7734992	Intron	5p15.33	Disease	> 0.01	Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer
TET2	rs17253672	Exon	4q24	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
TET2	rs9790517	Intron	4q24	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
TET2	rs9790517	Intron	4q24	Disease	> 0.01	Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk
TET2-AS1	rs17253672	Intron	4q24	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
TET2	rs62331150	Intron	4q24	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TEX10	rs10124893	Intron	9q31.1	Disease	> 0.01	A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia
TEX15	rs760604179	Exon	8p12	Disease	< 0.01	Case-control analysis of truncating mutations in DNA damage response genes connects TEX15 and FANCD2 with hereditary breast cancer susceptibility
TGFB1	rs1800470	Exon	19q13.2	Disease	> 0.01	A common coding variant in CASP8 is associated with breast cancer risk
TGFB1	rs1800470	Exon	19q13.2	Disease	> 0.01	Commonly Studied Single-Nucleotide Polymorphisms and Breast Cancer: Results From the Breast Cancer Association Consortium
TGFB1	rs1800470	Exon	19q13.2	Protective	> 0.01	Association Study of Transforming Growth Factor Beta 1 + 29 T/C exon 1 Polymorphism in Breast Cancer Patients from North Indian Population
TGFBR1	rs11466445	Exon	9q22.33	Disease	> 0.01	Transforming Growth Factor beta Receptor 1 Polyalanine Polymorphism and Exon 5 Mutation Analysis in Breast and Ovarian Cancer
TGFBR2	rs12493607	Intron	3p24.1	Disease	> 0.01	Large-scale genotyping identifies 41 new loci associated with breast cancer risk
TGFBR2	rs12493607	Intron	3p24.1	Disease	> 0.01	Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population
TGFBR2	rs12493607	Intron	3p24.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TGIF2LX	-	Exon	Xq21.31	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
TINF2	rs201677741	Exon	14q12	Disease	< 0.01	Truncating TINF2 p.Tyr312Ter variant and inherited breast cancer susceptibility
TLN2	rs956006	Intron	15q22.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TLR1	rs5743618	Exon	4p14	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TLR6	rs5743810	Exon	4p14	Protective	> 0.01	Novel sequence variants in the TLR6 gene associated with advanced breast cancer risk in the Saudi Arabian population
TLR9	rs352140	Exon	3p21.2	Protective	> 0.01	Genetic variation in TLR or NFkappaB pathways and the risk of breast cancer: a case-control study
TNFSF11	rs9533156	Intron	13q14	Disease	> 0.01	Risk association of RANKL and OPG gene polymorphism with breast cancer to bone metastasis in Pashtun population of Khyber Pakhtunkhwa, Pakistan
TNFSF4	rs3861950	Intron	1q25.1	Disease	> 0.01	A genome-wide association study of breast cancer in women of African ancestry
TNNT3	-	-	11p15.5	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
TNNT3	rs909116	Intron	11p15.5	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
TNPO1-DT	rs3010266	Intron	5q13.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TOGARAM2	rs56158184	Intron	2p23.2	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TOX3	-	Exon	16q12.1	Disease	-	A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
TOX3	rs12443621	Intron	16q12.1	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
TOX3	rs8051542	Intron	16q12.1	Disease	> 0.01	Genome-wide association study identifies novel breast cancer susceptibility loci
TP53	-	Exon	17p13.1	Disease	< 0.01	Spectrum of Mutations in BRCA1, BRCA2, CHEK2, and TP53 in Families at High Risk of Breast Cancer
TP53	-	Exon	17p13.1	Disease	< 0.01	Germline p53 Mutations in a Cohort with Childhood Sarcoma: Sex Differences in Cancer Risk
TP53	-	Exon	17p13.1	Disease	< 0.01	Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women
TP53	-	Exon	17p13.1	Disease	-	Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
TP53	-	Exon	17p13.1	Disease	-	Evaluating breast cancer predisposition genes in women of African ancestry
TP53	rs1042522	Exon	17p13.1	Protective	> 0.01	Impact of p53 arg72pro SNP on Breast Cancer Risk in North Indian Population
TP53	rs1042522	Exon	17p13.1	Disease	> 0.01	Significant association of BRCA1 (rs1799950), BRCA2 (rs144848) and TP53 (rs1042522) polymorphism with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan
TP53	rs1042522	Exon	17p13.1	Disease	> 0.01	Association between the Arg72Pro Genotypes in the TP53 Gene and Ile655Val in the HER2 Gene and the Risk of Developing Breast Cancer in the Population of Amapá, Northern Brazil
TP53	rs17878362	Intron	17p13.1	Disease	> 0.01	Intron 3 16 bp duplication polymorphism of p53 is associated with an increased risk for breast cancer by the age of 50 years
TP53	rs121912664	Exon	17p13.1	Disease	< 0.01	Detection of germline variants in Brazilian breast cancer patients using multigene panel testing
TPTE2	-	Exon	13q12.11	Disease	< 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
TRDN	-	CNV	6q22.31	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
TRIM46	rs4971059	Intron	1q22	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
TRIM6	-	CNV	11p15.4	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
TRPS1	rs13277568	Intron	8q23.3	Protective	> 0.01	Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
TRPS1	rs13277568	Intron	8q23.3	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
TSPAN16	rs322144	Intron	19p13.2	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
TSPYL6	rs843706	3 Prime UTR Variant	2p16.2	Disease	> 0.01	Association between single nucleotide polymorphisms in the TSPYL6 gene and breast cancer susceptibility in the Han Chinese population
TXNRD2	rs2020917	Intron	22q11.21	Protective	> 0.01	Breast Cancer Risk Reduction and Membrane-Bound Catechol O-Methyltransferase Genetic Polymorphisms
TXNRD2	rs2075507	Intron	22q11.21	Protective	> 0.01	The Investigation of Functional Genetic Variation in COMT Gene Promoter (rs2020917 & rs2075507) in Iranian Patients with Breast Cancer
TopBP1	rs55633281	Exon	3q22.1	Disease	> 0.01	Identification of a Common Polymorphism in the TopBP1 Gene Associated With Hereditary Susceptibility to Breast and Ovarian Cancer
UGT1A	rs3064744	Exon	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A10	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A3	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A4	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A5	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A6	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A7	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A8	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UGT1A9	rs3064744	Intron	2q37.1	Disease	> 0.01	Genetic Polymorphisms in Uridine Diphospho-Glucuronosyltransferase 1A1 and Association with Breast Cancer among African Americans
UNC13C	rs12908083	Intron	15q21.3	Disease	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
USHBP1	rs7246243	Intron	19p13.11	Disease	> 0.01	Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
USP18	-	CNV	22q11.2	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
USP31	-	CNV	16p12.2	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
VDR	rs1544410	Intron	12q13.11	Disease	> 0.01	Vitamin D receptor genotype and breast cancer in Latinas (United States)
VDR	rs2228570	Initiator Codon Variant	12q13.11	Disease	> 0.01	Vitamin D Receptor Polymorphisms and Breast Cancer Risk: Results from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium
VDR	rs2228570	Initiator Codon Variant	12q13.11	Disease	> 0.01	FokI polymorphism of Vitamin D receptor gene and deficiency of serum Vitamin D increases the risk of breast cancer in North Indian women
VDR	rs7975232	Intron	12q13.11	Disease	> 0.01	Association of a vitamin D receptor polymorphism with sporadic breast cancer development
VDR	rs731236	Exon	12q13.11	Disease	> 0.01	Lower vitamin D levels and VDR variants are risk factors for breast cancer: an updated meta-analysis
VDR	rs7975232	Intron	12q13.11	Disease	> 0.01	Associations of vitamin D receptor encoding gene variants with premenopausal breast cancer risk
VGLL3	rs13066793	Intron	3p12.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
VGLL3	rs13066793	Intron	3p12.1	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
VPS53	-	CNV	17p13.3	Protective	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
WDR43	rs4577244	Intron	2p23.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
WDR43	rs4577244	Intron	2p23.2	Protective	> 0.01	Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
WDR43	rs67073037	Intron	2p23.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
WDR43	rs6734079	Intron	2p23.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
WRAP53	rs2287499	Exon	17p13.1	Disease	> 0.01	Common Genetic Variation in TP53 and Its Flanking Genes, WDR79 and ATP1B2, and Susceptibility to Breast Cancer
WRN	rs1346044	Exon	8p12	Disease	> 0.01	Association of the rs1346044 Polymorphism of the Werner Syndrome Gene RECQL2 with Increased Risk and Premature Onset of Breast Cancer
WTAPP1	rs1144393	Intron	11q22.2	Protective	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
WTAPP1	rs1799750	Intron	11q22.2	Disease	> 0.01	Synergistic effect of collagenase-1 (MMP1), stromelysin-1 (MMP3) and gelatinase-B (MMP9) gene polymorphisms in breast cancer
WTAPP1	rs5854	Intron	11q22.2	Protective	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
WTAPP1	rs7125062	Intron	11q22.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
WTAPP1	rs996999	Intron	11q22.2	Disease	> 0.01	Matrix Metalloproteinase Genes Are Associated with Breast Cancer Risk and Survival: The Breast Cancer Health Disparities Study
XPA	rs1800975	Non Coding Transcript Variant	9q22.33	Protective	> 0.01	Nucleotide excision repair pathway gene polymorphisms are linked to breast cancer risk in a Chinese population
XPC	rs2228000	Exon	3p25.1	Disease	> 0.01	Nucleotide excision repair pathway gene polymorphisms are linked to breast cancer risk in a Chinese population
XPC	rs2228001	Exon	3p25.1	Protective	> 0.01	Nucleotide excision repair pathway gene polymorphisms are linked to breast cancer risk in a Chinese population
XRCC1	rs1799782	Exon	19q13.31	Protective	> 0.01	Genetic Polymorphisms in Base-Excision Repair Pathway Genes and Risk of Breast Cancer
XRCC1	rs25487	Exon	19q13.31	Protective	> 0.01	Genetic Polymorphisms in Base-Excision Repair Pathway Genes and Risk of Breast Cancer
XRCC1	rs25487	Exon	19q13.31	Protective	> 0.01	Genetic Variations of DNA Repair Genes in Breast Cancer
XRCC1	rs25487	Exon	19q13.31	Disease	> 0.01	The interplay between XPG-Asp1104His polymorphism and reproductive risk factors elevates risk of breast cancer in Tanzanian women: A multiple interaction analysis
XRCC1	rs25489	Exon	19q13.31	Disease	> 0.01	Genetic polymorphisms in the DNA repair genes XRCC1, XRCC2 and XRCC3 and risk of breast cancer in Cyprus
XRCC2	-	Exon	7q36.1	Disease	< 0.01	Rare mutations in XRCC2 increase the risk of breast cancer
XRCC2	rs3218536	Exon	7q36.1	Protective	> 0.01	Polymorphisms in DNA double-strand break repair genes and risk of breast cancer: two population-based studies in USA and Poland, and meta-analyses
XRCC2	rs3218536	Exon	7q36.1	Protective	> 0.01	Genetic polymorphisms in the DNA repair genes XRCC1, XRCC2 and XRCC3 and risk of breast cancer in Cyprus
XRCC2	rs3218536	Exon	7q36.1	Protective	> 0.01	Common single-nucleotide polymorphisms in DNA double-strand break repair genes and breast cancer risk
XRCC2	rs3218536	Exon	7q36.1	Disease	> 0.01	Correlation between Selected XRCC2, XRCC3 and RAD51 Gene Polymorphisms and Primary Breast Cancer in Women in Pakistan
XRCC3	rs1799796	Intron	14q32.33	Protective	> 0.01	Variants in DNA double-strand break repair genes and breast cancer susceptibility
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	Variants in DNA double-strand break repair genes and breast cancer susceptibility
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	Correlation between selected XRCC2, XRCC3 and RAD51 gene polymorphisms and primary breast cancer in women in Pakistan
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	Genetic Variations of DNA Repair Genes in Breast Cancer
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	Relationship between polymorphisms in homologous recombination repair genes RAD51 G172T、XRCC2 & XRCC3 and risk of breast cancer: A meta-analysis
XRCC3	rs861539	Exon	14q32.33	Disease	> 0.01	The interplay between XPG-Asp1104His polymorphism and reproductive risk factors elevates risk of breast cancer in Tanzanian women: A multiple interaction analysis
XRCC3	rs861539	Exon	14q32.33	Protective	> 0.01	Association of RAD51, XRCC1, XRCC2, and XRCC3 Polymorphisms with Risk of Breast Cancer
XRCC5	rs3835	Intron	2q35	Disease	> 0.01	Polymorphisms in Nonhomologous End-Joining Genes Associated with Breast Cancer Risk and Chromosomal Radiosensitivity
XRCC6	rs73161324	Intron	22q13.2	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
XRCC6	rs73161324	Intron	22q13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZBED6	rs59867004	Intron	1q32.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZBTB38	rs34207738	Intron	3q23	Disease	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ZBTB38	rs6440006	Intron	3q23	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZC3H11A	rs4951011	Intron	1q32.1	Disease	> 0.01	Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1
ZC3H11A	rs59867004	Intron	1q32.1	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZFPM2	rs12546444	Intron	8q23.1	Protective	> 0.01	Association analysis identifies 65 new breast cancer risk loci
ZFPM2	rs12546444	Intron	8q23	Protective	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZMIZ1	rs704010	Intron	10q22.3	Disease	> 0.01	Association of multiple genetic variants with breast cancer susceptibility in the Han Chinese population
ZMIZ1	rs704010	Intron	10q22.3	Disease	> 0.01	Genetic susceptibility loci for subtypes of breast cancer in an African American population
ZMIZ1	rs704010	Intron	10q22.3	Disease	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
ZMIZ1	rs704010	Intron	10q22.3	Disease	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
ZMIZ1	rs704010	Intron	10q22.3	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
ZNF320	-	CNV	19q13.41	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
ZNF365	rs10995190	Intron	10q21.2	Protective	> 0.01	Genome-wide association study identifies five new breast cancer susceptibility loci
ZNF365	rs10995190	Intron	10q21.2	Protective	> 0.01	Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
ZNF365	rs10995190	Intron	10q21.2	Protective	> 0.01	Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast
ZNF365	rs10995201	Intron	10q21.2	Protective	> 0.01	Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression
ZNF404	-	-	19q13.31	Disease	-	Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
ZNF439	-	CNV	19p13.2	Disease	< 0.01	Rare germline copy number variants (CNVs) and breast cancer risk
ZNF479	rs200382632	Exon	7p11.2	Disease	> 0.01	Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility
ZNF577	rs10411161	Intron	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
ZNF577	rs11878583	Intron	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
ZNF577	rs3848562	Intron	19q13.41	Disease	> 0.01	Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
ZNF805	rs7248000	Intron	19q13.43	Protective	> 0.01	Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium
ZSCAN25	rs776746	Intron	2p22.2	Disease	> 0.01	Genetic polymorphisms in estrogen metabolism and breast cancer risk in case–control studies in Japanese, Japanese Brazilians and non-Japanese Brazilians
ZZEF1	rs2123844	Intron	17p13.2	Disease	> 0.01	Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics