After applying variant filters and obtaining our final meta-analytic results, we calculated genomic controls and maximum/median per-variant sample sizes. Sample sizes ranged from 337,334 for cigarettes per day to 1,232,091 for smoking initiation. QQ plots, LD intercept tests, and genomic control values indicate that Type I error rates were well controlled, for common and low-frequency variants (Supplementary Figure 2, Supplementary Table 26). All conditionally independent variants were plotted in LocusZoom and included in Supplementary Figures 1–12. All plots were visually inspected, suspicious loci were identified (see Supplementary Table 27) and removed from further consideration. To ensure LD information was available between sentinel variants and others in the locus, we used surrogate variants for eight loci (Supplementary Table 28).
