To investigate whether the association with cotinine at 15q25.1 could be explained completely by rs10851907, we repeated the association analysis conditioning on this SNP (Figure S2). Residual association was detected within the region, with strongest evidence for association at rs57064725 (pc = 2.92 × 10−8), located in an intron of PSMA4 (Figure S2, middle panel). Conditioning on both of these variants left no residual signal (Figure S2, bottom panel). Given previous robust evidence linking measures of smoking quantity to the nonsynonymous SNP rs16969968, a variant which also exceeded the threshold for genome-wide significance in our analyses (p = 6.91 × 10−17), we also re-ran the association analysis conditioning on this SNP (Figure S3). Residual association similar to that observed after conditioning on rs10851907 was detected within the region, with strongest evidence for association at rs7170068 (pc = 1.51 × 10−9), located in an intron in CHRNA3 (Figure S3, middle panel). Conditioning on rs16969968 and rs7170068 left no residual signal in this region (Figure S3, bottom panel). It is notable that earlier dissection of the 15q25.1 region has suggested a third
