Table 1. Association of the two most strongly associated SNPs (rs4442975 and rs6721996) and the original GWAS SNP (rs13387042) with breast cancer.
SNP | Position | Ref | Alt | EAF * | OR_overall | P1df_overall | OR_ER- | P1df_ER- | OR_ER+ | P1df_ER+ |
---|---|---|---|---|---|---|---|---|---|---|
Europeans | ||||||||||
rs4442975 | 217920769 | G | T | 0.49 | 0.87 (0.86–0.89) | 3.91E−46 | 0.95 (0.91–0.98) | 0.0043 | 0.85 (0.84–0.87) | 1.69E−43 |
rs6721996 | 217909463 | G | A | 0.49 | 0.87 (0.86–0.89) | 7.09E−45 | 0.94 (0.91–0.98) | 0.0028 | 0.86 (0.84–0.88) | 4.02E−42 |
rs13387042 | 217905832 | A | G | 0.51 | 0.88 (0.86–0.89) | 1.69E−41 | 0.96 (0.92–0.99) | 0.023 | 0.86 (0.84–0.88) | 5.63E−40 |
Asians | ||||||||||
rs4442975 | 217920769 | G | T | 0.13 | 0.94 (0.87–1.02) | 0.12 | 1.01 (0.89–1.14) | 0.90 | 0.93 (0.85–1.02) | 0.11 |
rs6721996 | 217909463 | G | A | 0.12 | 0.95 (0.88–1.03) | 0.20 | 1 (0.89–1.14) | 0.96 | 0.94 (0.86–1.03) | 0.20 |
rs13387042 | 217905832 | A | G | 0.12 | 0.95 (0.88–1.03) | 0.21 | 1.01 (0.89–1.14) | 0.89 | 0.94 (0.85–1.03) | 0.18 |
Alt, alternative; ER, oestrogen receptor; GWAS, genome-wide association study; OR, odds ratio; Ref, reference; SNP, single nucleotide polymorphism.
The table displays the per-allele odds ratios for breast cancer in Europeans and Asians, and separately for ER-positive and ER-negative disease. In the Asian studies, the protective/rare alleles for these three SNPs are rarer (minor allele frequencies (MAFs)=0.13, 0.12 and 0.12, respectively) than in Europeans (MAF=0.49) but their associated relative risk estimates with overall breast cancer are consistent: per-t-allele OR (rs4442975)=0.94; 95% confidence interval (CI) -0.87 to 1.02; P=0.12; per-a-allele OR (rs6721996)=0.95; 95% CI -0.88 to 1.03; P=0.20; and per-a-allele OR (rs13387042)=0.95; 95% CI -0.88 to 1.03; P=0.21.
*EAF, effect allele frequency (frequency of the alternative allele relative to the reference allele).