and rs720475) for which the heterozygotes had a similar OR as homozygotes for the high-risk allele and two SNPs (rs11242675 and rs6472903) that were more consistent with a recessive model (Supplementary Table 6). Consistent with the pattern seen for previously established loci, there was strong evidence for specificity of the association to tumor subtype. For 13 of the loci, the per-allele OR was higher for ER-positive disease than for ER-negative disease (case-only P < 0.05), in most instances with little or no evidence of an association with ER-negative disease (based on data from 7,465 ER-negative cases and 27,074 ER-positive cases; Supplementary Table 7a). The most notable differences were for SNP rs6828523 at 4q34.1 (ER-positive OR = 0.87 (95% confidence interval (CI) = 0.84–0.90); ER-negative OR = 1.01 (95% CI = 0.96–1.07); P for difference = 1.2 × 10−7) and for rs7072776 at 10p12.31, where the estimated effects were in opposite directions (ER-positive OR = 1.09 (95% CI = 1.06–1.12); ER-negative OR = 0.94 (95% CI = 0.90–0.98); P for difference = 3.1 × 10−10). No such difference was observed for the neighboring SNP rs11814448, which was associated with both ER-positive and ER-negative disease in the same direction. For one locus,
