Table 2. Summary of results for eleven SNPs selected for stage 3 that showed evidence of an association with breast cancer.
| rs Number | Gene | Position* | m.a.f.† | Per allele OR (95% CI) |
HetOR (95% CI) |
HomOR (95% CI) |
P-trend |
||
|---|---|---|---|---|---|---|---|---|---|
| Stages 1 and 2 |
Stage3 | Combined | |||||||
| rs2981582 | FGFR2 | 10q 123342307 |
0.38 (0.30) |
1.26 (1.23–1.30) |
1.23 (1.18–1.28) |
1.63 (1.53–1.72) |
4×10−16 | 5×10−62 | 2×10−76 |
| rs12443621 |
TNRC9/ LOC643714 |
16q 51105538 |
0.46 (0.60) |
1.11 (1.08–1.14) |
1.14 (1.09–1.20) |
1.23 (1.17–1.30) |
10−7 | 9×10−14 | 2×10−19 |
| rs8051542 |
TNRC9/ LOC643714 |
16q 51091668 |
0.44 (0.20) |
1.09 (1.06–1.13) |
1.10 (1.05–1.16) |
1.19 (1.12–1.27) |
4×10−6 | 4×10−8 | 10−12 |
| rs889312 | MAP3K1 | 5q 56067641 |
0.28 (0.54) |
1.13 (1.10–1.16) |
1.13 (1.09–1.18) |
1.27 (1.19–1.36) |
4×10−6 | 3×10−15 | 7×10−20 |
| rs3817198 | LSP1 | 11p 1865582 |
0.30 (0.14) |
1.07 (1.04–1.11) |
1.06 (1.02–1.11) |
1.17 (1.08–1.25) |
8×10−6 | 10−5 | 3×10−9 |
| rs2107425 | H19 | 11p 1977651 |
0.31 (0.44) |
0.96 (0.93–0.99) |
0.94 (0.90–0.98) |
0.95 (0.89–1.01) |
7×10−6 | 0.01 | 2×10−5 |
| rs13281615 | 8q 128424800 |
0.40 (0.56) |
1.08 (1.05–1.11) |
1.06 (1.01–1.11) |
1.18 (1.10–1.25) |
2×10−7 | 6×10−7 | 5×10−12 | |
|
| |||||||||
| rs981782 | 5p 45321475 |
0.47 (0.37) |
0.96 (0.93–0.99) |
0.96 (0.92–1.01) |
0.92 (0.87–0.97) |
8×10−5 | 0.003 | 9×10−6 | |
| rs30099 | 5q 52454339 |
0.08 (0.39) |
1.05 (1.01–1.10) |
1.06 (1.00–1.11) |
1.09 (0.96–1.24) |
0.003 | 0.02 | 0.001 | |
| rs4666451 | 2p 19150424 |
0.41 (0.04) |
0.97 (0.94–1.00) |
0.98 (0.93–1.02) |
0.93 (0.87–0.99) |
5×10−6 | 0.04 | 6×10−5 | |
|
| |||||||||
| rs3803662‡ |
TNRC9/ LOC643714 |
16q 51143842 |
0.25 (0.60) |
1.20 (1.16–1.24) |
1.23 (1.18–1.29) |
1.39 (1.26–1.45) |
3×10−12 | 10−26 | 10−36 |
OR, odds ratio; HetOR, odds ratio in heterozygotes; HomOR, odds ratio in rare homozygotes (relative to common homozygotes); CI, confidence interval.
*
Build 36.2 position.
†
Minor allele frequency in SEARCH (UK) study. Combined allele frequency from three Asian studies in italics.
‡
rs3803662 was not part of the initial tag SNP set but identified as a result of fine-scale mapping of the TNRC9/LOC643714 locus and typed in the stage 2 and stage 3 sets (but not the stage 1 set).