Although the associations with breast cancer were of similar magnitude and direction for most SNPs when comparing the two datasets, the risk of breast cancer associated with rs352140 in TLR9 was in the opposite direction (OR 1.06, 95% CI 0.94–1.19) from that found in our data (OR 0.85, 95% CI 0.74–0.97). Here, TLR9 is linked to breast carcinoma.