Table 1.
The Best Candidate Variants Representing the Four iCHAVs with the Strongest Effects on Breast Cancer Risk in European Studies
| iCHAV | SNP | Chr Position (GRch37) | Alleles (Major/Minor) | MAF | r2with Lead iCHAV1 SNP | Imputation r2 |
Overall Breast Cancer Risk |
ER+Breast Cancer Risk |
ER−Breast Cancer Risk |
ER Status |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR | (95% CI) | ptrend | pcond | OR | (95% CI) | ptrend | pcond | OR | (95% CI) | ptrend | pcond | pdiff | |||||||
| 1 | rs62355902 | 56,053,723 | A/T | 0.18 | – | 0.95 | 1.21 | (1.19–1.24) | 9.50 × 10−49 | – | 1.24 | (1.21–1.27) | 5.71 × 10−44 | – | 1.10 | (1.05–1.15) | 3.02 × 10−4 | – | 1.47 × 10−5 |
| 2a | rs113317823 | 56,087,883 | C/T | 0.08 | 0.19 | 0.72 | 1.22 | (1.18–1.26) | 7.00 × 10−25 | 1.61 × 10−5 | 1.24 | (1.20–1.29) | 2.02 × 10−21 | 9.74 × 10−5 | 1.12 | (1.05–1.20) | 2.56 × 10−3 | 9.90 × 10−2 | 1.93 × 10−2 |
| 2b | rs62355899 | 56,050,465 | A/G | 0.13 | 0.62 | 1.00 | 1.15 | (1.12–1.18) | 2.98 × 10−19 | 3.04 × 10−5 | 1.17 | (1.13–1.20) | 5.52 × 10−18 | 2.04 × 10−3 | 1.08 | (1.02–1.14) | 1.11 × 10−2 | 5.42 × 10−1 | 1.86 × 10−2 |
| 3 | rs11949391 | 56,045,081 | T/C | 0.16 | 0.04 | 1 | 0.91 | (0.89–0.94) | 9.36 × 10−12 | 5.57 × 10−5 | 0.90 | (0.87–0.93) | 1.00 × 10−10 | 1.44 × 10−4 | 1.01 | (0.96–1.06) | 8.14 × 10−1 | 3.50 × 10−1 | 1.27 × 10−4 |
Single-SNP risk estimates for the top candidates in each iCHAV as well as overall breast cancer risk and subtypes by estrogen receptor status. Results are given as ORs with 95% CI (with the minor variant alleles as the reference), per-allele ptrend, and pcond (pcond is conditional on the iCHAV1 lead SNP rs62355902). The pdiff for ER status is from a case-only analysis comparing the effect sizes between the ER+ and ER− subtypes. The complete list of variants for these iCHAVs can be found in Table S7).