In European-ancestry populations, each of the four loci of interest can be represented by various highly correlated SNPs (SNPs having high r2 with each other). For each locus, we chose one target SNP for analysis: rs16969968 (locus 1), rs578776 (locus 2), rs588765 (locus 3), and rs12914008 (locus 4); the pairwise correlations between any two of these loci are r2<0.5 (Table S1). In samples for which a given target SNP was not available, we chose a highly correlated proxy SNP based on r2 computed with Haploview [26] using downloaded HapMap CEU genotype data, Release 23 [27]. Table S2 lists the proxy SNPs used and their r2 with the corresponding target SNPs. Figure S1 displays the SNPs for each of the 4 loci in relation to the CHRNA5-CHRNA3-CHRNB4 cluster.
