To control for possible confounding due to population stratification, we estimated individual ancestry proportions for each subject, which were then used as covariates in the regression model. A panel of 41 ancestry informative markers (AIMs), including 36 highly ancestry-informative short tandem repeat markers and 5 SNPs (rs1540771, rs2814778, rs1805007, rs1426654 and rs12896399) were genotyped in a majority of subjects (93.4%), among which 1592 AAs and 1093 EAs with genotyping rate > 50% were further included to estimate the individual admixture proportion. The exact sample size for each phenotype analyzed with admixture proportion as a covariate is provided in Supplementary table 1. Detailed genotyping methods for 37 of the 41 AIMs (including an FY SNP) have been described in detail previously (Yang et al., 2005). The remaining four SNPs were genotyped by the same TaqMan technique as was used for the CHRNA4 SNPs. We used the STRUCTURE program (Pritchard et al., 2000) to estimate the admixture proportion for each individual based on the AIMs. The log-likelihood of each analysis at a different number of population groups (k) was estimated from the
