Because FTO was GWS for both AUDIT-C and AUD, we repeated the two GWASs correcting for body mass index (BMI). Among the top SNPs associated with AUDIT-C and AUD, most remain GWS after correction for BMI, though the significance level of some change (Supplementary Data 9, 10). FTO SNPs become only nominally significant for both alcohol-related traits: the p value for the lead SNP for AUDIT-C, rs9937709, decreases in significance from 5.53 × 10−14 to 1.42 × 10−5 and for the lead SNP for AUD, rs11075992, it decreases in significance from 3.22 × 10−10 to 3.02 × 10−5. In contrast, with correction for BMI, some signals increase, e.g., for rs1260326 in GCKR the p value increases in significance from p = 2.04 × 10−16 to p = 2.91 × 10−19 for AUDIT-C and from p = 2.27 × 10−13 to p = 1.71 × 10−14 for AUD. Similarly, rs1229984 in ADH1B increases in significance from p = 3.62 × 10−133 to p = 9.81 × 10−145 for AUDIT-C and from p = 4.68 × 10−85 to p = 3.85 × 10−89 for AUD.
