The interaction of rs3858704-A in the ALDH2 region of chromosome 12 with consumption of ≥ 7 drinks per week was significant in Phase 1, but neither that variant nor any proxies with r2 ≥ 0.7 were available in the Phase 2 data (Additional file 1: Table S2).We found a previously unreported association of rs79865122-C on chromosome 10 near CYP2E1 with odds of ER- and PR- breast cancer, including a statistically significant joint main plus interaction effect. This evidence concerns the gene CYP2E1 and breast cancer.