Table 2.

Locus-specific ancestry (LSA) association adjusting for multiple SNPs

Multi-SNP model				Single-SNP association
SNP id	Position	ORa	P-valueb	Allelesc	Allele freqd	ORe	P-value
LSA 6q25		0.74	9.42×106
s79692348	151937679	0.82	0.0099	C/T	0.87 (0.99)	1.52	2.10×106
rs4304175	151923982	0.83	0.0134	T/C	0.41 (0.30)	0.79	2.60×105
rs9383928	151896937	0.84	0.0178	A/G	0.72 (0.79)	1.30	2.90×105
rs7747474	149565986	0.88	0.0955	T/C	0.12 (0.25)	1.44	3.00×105
LSA 11p15		0.77	3.81×105
rs10444227	19945852	0.83	0.0051	A/C	0.70 (0.52)	0.76	6.40×106
rs4757841	19767614	0.89	0.0915	A/G	0.39 (0.49)	1.26	4.20×105

^aOR shows effect of LSA per chromosome.

^bThese are the P-values for the effect of LSA in the model with no adjustment and the models adjusting for multiple SNPs.

^cTested allele/reference allele.

^dAllele frequency for the tested allele in US Latinas (in parenthesis is the frequency in Europeans, Supplementary Material, Table S4).

^eOR per allele for each SNP (per allele) and breast cancer risk.