Ten SNPs in CHRNA5/A3/B4 were genotyped using Taq-Man® assays for allelic discrimination (Applied Biosystems) per manufacturer’s instructions using an ABI PRISM® 7900 instrument. SNPs were selected based on validation status, minor allele frequency greater than 0.10, and location in the gene to be approximately evenly distributed. The SNPs used in this study were selected for a previous study (Schlaepfer et al. 2008), and the selection was made prior to availability of much linkage disequilibrium (LD) data on HapMap (www.hapmap.org), but a comparison to other studies (Saccone et al. 2010) suggests the three major LD signals (locus 1, locus2, and locus 3) in the region are captured by the ten selected SNPs. The selected SNPs (in order along the physical map of the gene cluster) were rs684513, rs680244, rs16969968, rs514743, rs11637630, rs8040868, rs8023462, rs1948, rs1316971, and rs11634351. Two of these SNPs (rs16969968 and rs8040868) tag the locus 1 signal defined by Saccone et al. (2009a, b, 2010). One SNP (rs11637630) tags locus 2, and two SNPs (rs680244 and rs514743) tag locus 3. The other SNPs appear to be separate LD signals
