We tested the 23 CHRNA4 SNPs/indels associated with nicotine dependence at P<5 × 10−5 for independent replication using 7469 ever smokers from five European-ancestry samples (Table 1 and Supplementary Table 5). Two SNPs had genome-wide significant associations with nicotine dependence across all the samples (Table 2): rs2273500 and rs6011779, which are in strong linkage disequilibrium in European-ancestry individuals (D′=1.00 and r2=0.70, Figure 1b and Supplementary Figure 3). Their minor alleles (frequency=0.15 and 0.20) were associated with greater nicotine dependence risk, as demonstrated in Figure 2 for the top SNP rs2273500: meta-analysis odds ratio=1.06 (95% confidence interval 1.04–1.08) for moderate vs mild nicotine dependence and odds ratio=1.12 (95% confidence interval 1.08–1.17) for severe vs mild nicotine dependence. None of the tested SNPs/indels showed significant evidence for between-sample heterogeneity (Supplementary Table 6).
