We analyzed 144 SNPs covering the 13 CHRN genes outside chromosome 15q25; SNPs were selected to match those covered in the previously reported subjects (Bierut et al., 2007, Saccone et al., 2009a, Saccone et al., 2007). SNPs were genotyped using Illumina Golden Gate and Sequenom iPlex technologies. All DNA samples had call rates above 90% across the genotyped SNPs and 99.5% of DNA samples had call rates ≥ 95%; Illumina-based SNPs (N=133) passed a call rate threshold of 98% and Sequenom-based SNPs (N=11) satisfied a call rate threshold of 95%. Self-reported race was verified with an EIGENSTRAT (Price et al., 2006) principal components analysis of 162 ancestry informative markers genotyped both in our samples and in the HapMap CEU, YRI and HCB-JPT samples which were included as anchors. Map positions and genomic annotations were obtained from the National Center for Biotechnology Information (NCBI) Human Reference Build 36.2 and dbSNP build 129.
