Table 4. Associations of the most significantly associated SNPs from the discovery set s with disease free survival (adjusted for ER-status).
| Lead SNP | Chr | Position | Alleles | MAF | Stage −1 association(95%Confidence Interval) | HEBC associations | Stage-2 association (95%ConfidenceInterval) | All stages meta-analysis p-value | p-value for Q-statistic |
| rs7441398 | 4 | 63653135 | G/T | 0.13 | 1.41 (1.12–1.77) | 1.11 (0.88–1.42) | 1.07 (0.91–1.26) | 0.01 | 0.15 |
| rs1525677 | 7 | 110302695 | T/C | 0.31 | 1.21 (1.0–1.45) | 1.14 (0.96–1.35) | 1.05 (0.88–1.24) | 0.02 | 0.56 |
| rs12358475 | 10 | 11848792 | G/A | 0.23 | 0.83 (0.67–1.02) | 0.78 (0.65–0.94) | 0.86 (0.70–1.05) | 0.001 | 0.77 |
| rs2921923 | 10 | 55662089 | A/G | 0.49 | 1.42 (1.19–1.71) | 1.31 (1.12–1.52) | 1.08 (0.91–1.27) | 3.9×10−6 | 0.08 |
| rs10777864 | 12 | 97838685 | A/C | 0.41 | 0.80 (0.66–0.96) | 0.72 (0.60–0.85) | 1.07 (0.91–1.26) | 0.005 | 0.003 |
| rs8060556 | 16 | 6868511 | C/T | 0.23 | 1.20 (0.97–1.48) | 1.30 (1.07–1.57) | 0.94 (0.77–1.15) | 0.03 | 0.06 |
| rs1728400 | 16 | 86434446 | C/A | 0.38 | 1.27 (1.07–1.52) | 1.21 (1.03–1.41) | 1.17 (0.99–1.38) | 5.7×10−5 | 0.81 |
| rs8045253 | 16 | 86437767 | T/C | 0.34 | 1.27 (1.07–1.51) | 1.26 (1.07–1.48) | 0.90 (0.75–1.06) | 0.009 | 0.006 |
| rs421379 | 5 | 91275313 | G/A | 0.08 | 1.69 (1.24–2.30) | 1.04 (0.76–1.43) | 1.32 (0.90–1.93) | 0.003 | 0.10 |
Results are presented for those SNPs which remained associated in the same direction in the replication set as in the discovery set.