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.