Table 2 Single-nucleotide polymorphisms (SNPs) in the breast cancer study set. Allele frequencies, genotype frequencies and genotype-specific risks in 2343 women with breast cancer and 2284 controls. OR, odds ratio; CI, confidence intervals; RAF, rare allele frequency; M/M, common homozygotes; M/m, heterozygotes; m/m, rare homozygotes; df, degrees of freedom.
SNP | Series | RAF | M/M n (%) | M/m n (%) | m/m n (%) | Number genotyped | P 2 df |
|---|---|---|---|---|---|---|---|
5'up t>g | Cases | 0.33 | 989 (45) | 961 (44) | 231 (11) | 2181 | Â |
| Â | Controls | 0.32 | 1069 (47) | 959 (42) | 249 (11) | 2277 | 0.42 |
|  | OR (95% CI) |  | 1 (ref) | 1.08 (0.96–1.23) | 1.00 (0.82–1.22) |  |  |
IVS7 g>a | Cases | 0.40 | 727 (36) | 980 (48) | 317 (16) | 2024 | Â |
| Â | Controls | 0.40 | 803 (37) | 1025 (47) | 364 (16) | 2192 | 0.51 |
|  | OR (95% CI) |  | 1 (ref) | 1.06 (0.92–1.21) | 0.96 (0.80–1.15) |  |  |
IVS16 a>g | Cases | 0.13 | 1629 (75) | 502 (23) | 36 (2) | 2167 | Â |
| Â | Controls | 0.14 | 1690 (75) | 526 (23) | 42 (2) | 2258 | 0.87 |
|  | OR (95% CI) |  | 1 (ref) | 0.99 (0.86–1.14) | 0.89 (0.57–1.40) |  |  |
3'down c>t | Cases | 0.44 | 638 (32) | 986 (49) | 399 (20) | 2023 | Â |
| Â | Controls | 0.44 | 691 (31) | 1073 (49) | 440 (20) | 2204 | 0.98 |
|  | OR (95% CI) |  | 1 (ref) | 1.00 (0.87–1.14) | 0.98 (0.83–1.17) |  |  |
IVS9 a>g | Cases | 0.39 | 760 (37) | 988 (48) | 299 (15) | 2047 | Â |
| Â | Controls | 0.39 | 847 (39) | 1009 (46) | 343 (16) | 2199 | 0.29 |
|  | OR (95% CI) |  | 1 (ref) | 1.09 (0.96–1.24) | 0.97 (0.81–1.17) |  |  |
IVS10 c>t | Cases | 0.05 | 1824 (91) | 177 (9) | 3 (0) | 2004 | Â |
| Â | Controls | 0.04 | 1956 (91) | 187 (9) | 3 (0) | 2146 | 0.99 |
|  | OR (95% CI) |  | 1 (ref) | 1.02 (0.82–1.26) | 1.07 (0.22–5.32) |  |  |