Table 3. Replication of most significant associations from the discovery set meta-analysis in the replication samples.
| Lead SNP | Chr | Position | Alleles | MAF | Stage-2 replicationHR (95%Confidence Interval) | Stage-2replicationp-values | All stagesmeta-analysisHR(95%Confidence Interval) | All stages meta-analysisp-value | p-value for Q-statistic | Genes |
| rs7441398 | 4 | 63653135 | G/T | 0.13 | 1.12 (0.90–1.39) | 0.28 | 1.31 (1.15–1.49) | 3.3×10−5 | 0.21 | LPHN3: LOC644548 |
| rs1525677 | 7 | 110302695 | T/C | 0.31 | 1.08 (0.92–1.27) | 0.35 | 1.22 (1.10–1.34) | 0.0001 | 0.18 | IMMP2L |
| rs12358475 | 10 | 11848792 | G/A | 0.23 | 0.82 (0.67–1.00) | 0.05 | 0.75 (0.67–0.84) | 1.8×10−6 | 0.57 | ECHDC3: C10orf47 |
| rs2921923 | 10 | 55662089 | A/G | 0.49 | 1.03 (0.88–1.21) | 0.69 | 1.20 (1.10–1.33) | 0.0001 | 0.04 | PCDH15 |
| rs10777864 | 12 | 97838685 | A/C | 0.41 | 0.91 (0.77–1.07) | 0.25 | 0.82 (0.74–0.90) | 8.0×10−5 | 0.22 | RMST |
| rs8060556 | 16 | 6868511 | C/T | 0.23 | 1.01 (0.84–1.22) | 0.75 | 1.22 (1.09–1.36) | 0.001 | 0.04 | RBFOX1 |
| rs1728400 | 16 | 86434446 | C/A | 0.38 | 1.16 (0.99–1.37) | 0.07 | 1.25 (1.13–1.39) | 5.6×10−6 | 0.39 | LOC732275: FOXF1 |
| rs8045253 | 16 | 86437767 | T/C | 0.34 | 1.04 (0.88–1.23) | 0.65 | 1.17 (1.05–1.31) | 0.003 | 0.04 | LOC732275: FOXF1 |
| rs421379 | 5 | 91275313 | G/A | 0.08 | 1.41 (1.11–1.8) | 0.005 | 1.49 (1.27–1.75) | 1.1×10−6 | 0.09 | ARRDC3 |
Results are presented for those SNPs which remained associated in the same direction in the validation set as in the discovery set (adjusted for ER-status).