Table 1. Two independent association signals at the 1p11.2 locus: Association results for breast cancer risk among women in BCAC, by ancestry.
Signal | SNP | Positiona | Cases (N) | Controls (N) | Sourceb | Risk Allele | RAFc Cases/Controls | r2d | OR (95% CI)e | P-trend |
---|---|---|---|---|---|---|---|---|---|---|
European Ancestry | ||||||||||
1 | rs11249433 | 121280613 | 39,072 | 42,101 | G | G | 0.424/0.402 | ~ | 1.10 (1.08–1.13) | 1.49E-21 |
1.09 (1.06–1.11)f | 6.54E-15 | |||||||||
2 | rs146784183 | 121223447 | 39,072 | 42,101 | I | A | 0.906/0.899 | 0.086 | 0.88 (0.85–0.91) | 2.35E-12 |
0.92 (0.88–0.95)f | 1.27E-05 | |||||||||
Asian Ancestry | ||||||||||
1 | rs11249433 | 121280613 | 5,826 | 6,643 | G | G | 0.039/0.036 | ~ | 1.19 (1.04–1.36) | 0.01 |
2 | rs146784183 | 121223447 | 5,826 | 6,643 | I | A | 0.860/0.844 | 0.004 | 0.89 (0.82–0.96) | 0.002 |
aGenomic coordinates are based on hg19.
bSource indicates whether the SNP was genotyped (G) or imputed (I) within the data used from the 1000 Genomes Project.
cRisk allele frequency (RAF) for cases/controls.
dPair-wise linkage disequilibrium (r2) with the top SNP rs11249433 calculated using iCOGS (n = 84,396) data, for controls only.
ePer-allele odds ratios (OR) and 95% confidence intervals (95% CI) were estimated from logistic regression adjusted for study site and 7 principal components in Europeans and 2 principal components in women with Asian ancestry. The common allele was the referent for calculating odds ratio; the G-allele for both rs11249433 and rs146784183.
fOdds ratios (OR) and 95% confidence intervals (95% CI) were estimated from logistic regression mutually adjusted for rs146784183 and top SNP (rs11249433) along with study site and 7 principal components.