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).