Table 3.
Four FBC predisposition loci at which variants correlated at r2 ≥ 0.10 with a published FBC susceptibility SNP were more statistically significantly associated with MBC than the lead FBC SNP
| Cytoband | SNPa | Allelesb | Stage | Control MAF | Case MAF | OR (95% CI) | P c |
|---|---|---|---|---|---|---|---|
| 6q25.1 | rs3757322 | T/G | GWAS | 0.33 | 0.37 | 1.23 (1.12 to 1.35) | 1.11 × 10−05 |
| Replication | 0.33 | 0.39 | 1.32 (1.15 to 1.52) | 9.53 × 10−05 | |||
| Joint | — | — | 1.26 (1.16 to 1.36) | 6.23 × 10−09 | |||
| rs146723925 | GAA/G | GWAS | 0.35 | 0.39 | 1.23 (1.13 to 1.35) | 7.73 × 10−06 | |
| r 2 = 0.89 | Replication | — | — | Failed assay design | — | ||
| Joint | — | — | — | — | |||
| 6q25.1 | rs9397437 | G/A | GWAS | 0.07 | 0.10 | 1.58 (1.34 to 1.87) | 4.22 × 10−08 |
| Replication | 0.07 | 0.10 | 1.33 (1.05 to 1.69) | .02 | |||
| Joint | — | — | 1.50 (1.31 to 1.71) | 5.29 × 10−09 | |||
| rs9383938 | G/T | GWAS | 0.08 | 0.11 | 1.60 (1.36 to 1.89) | 1.63 × 10−08 | |
| r 2 = 0.83 | Replication | 0.09 | 0.11 | 1.30 (1.04 to 1.63) | .02 | ||
| Joint | — | — | 1.47 (1.30 to 1.67) | 2.93 × 10−09 | |||
| 10p12.31 | rs7072776 | G/A | GWAS | 0.27 | 0.30 | 1.17 (1.06 to 1.29) | .002 |
| Replication | 0.28 | 0.31 | 1.15 (0.99 to 1.33) | .06 | |||
| Joint | — | — | 1.16 (1.07 to 1.26) | 2.46 × 10−04 | |||
| rs2183271 | T/C | GWAS | 0.36 | 0.41 | 1.24 (1.13 to 1.36) | 3.50 × 10−06 | |
| r 2 = 0.68 | Replication | 0.36 | 0.40 | 1.18 (1.02 to 1.35) | .02 | ||
| Joint | — | — | 1.22 (1.13 to 1.31) | 2.69 × 10−07 | |||
| 11q13.3 | rs75915166 | C/A | GWAS | 0.06 | 0.08 | 1.52 (1.25 to 1.83) | 1.64 × 10−05 |
| Replication | 0.05 | 0.08 | 1.56 (1.19 to 2.04) | .001 | |||
| Joint | — | — | 1.53 (1.31 to 1.79) | 7.71 × 10−08 | |||
| rs78540526 | C/T | GWAS | 0.07 | 0.10 | 1.58 (1.34 to 1.87) | 7.38 × 10−08 | |
| r 2 = 0.63 | Replication | 0.06 | 0.10 | 1.68 (1.32 to 2.14) | 2.45 × 10−05 | ||
| Joint | — | — | 1.61 (1.40 to 1.85) | 1.06 × 10−11 |
For each locus the MBC effect estimates and association statistics for the lead FBC SNP are shown, followed by the estimates, correlation coefficient and association statistics for the correlated variant that was more strongly associated with MBC. CI = confidence interval; FBC = female breast cancer; GWAS = genome-wide association study; MAF = minor allele frequency; MBC = male breast cancer; OR = odds ratio; SNP = single nucleotide polymorphism.
Alleles are shown as major and minor alleles based on control frequencies.
MBC P values were derived from fixed-effects inverse variance-weighted meta-analysis (GWAS and joint) and from multiple logistic regression, adjusted for study (replication). All tests were 2-sided.
- Control and case MAFs were not calculated for meta-analyzed SNPs at the joint analysis stage.