Using our multi-ancestry meta-analysis, we identified 2,143 associated loci across all phenotypes (sentinel variant P < 5 × 10−9), with 3,823 independently associated variants (Extended Data Fig. 2, Supplementary Tables 2 and 3 and Supplementary Figs. 2 and 3). Of these, 1,346 loci and 2,486 independent variants were associated with SmkInit, 33 loci (39 variants) with AgeSmk, 140 loci (243 variants) with CigDay, 128 loci (206 variants) with SmkCes and 496 loci (849 variants) with DrnkWk. Approximately 64% (n = 1,364) of loci were phenotype-specific, five loci were associated with all four smoking phenotypes but not with DrnkWk, and five loci were associated with all five phenotypes. All sentinel variants within identified loci had high posterior probabilities that their effect would replicate in a sufficiently powered study according to a trans-ancestry extension of our GWAS cross-validation technique6. Only 17 sentinel variants (0.7%) had such posterior probabilities of less than 0.99 and were therefore removed from the counts above and from further consideration (additional details on these 17 variants are shown in Supplementary Fig. 4).
