To identify independent signals in each population, we performed LD clumping using PLINK v1.90b4.4 (ref. 48). We identified an index SNP (p < 5 × 10−8) with the smallest p value in a 500-kb genomic window and r2 < 0.1 with other index SNPs. Because in EAAs there is extended linkage disequilibrium at the ALDH2 locus, we used a 2500-kb window in that population. In the chr4q23–q24 region, where we identified multiple apparently independent signals for both AUDIT-C and AUD, we used conditional associations to differentiate independent signals from partially overlapping ones.
