GWAS analyses were performed using BGENIE v1.1 (18) with AUDIT scores (AUDIT total score, AUDIT-C, and AUDIT-P, tested independently) as the outcome variable and age, sex, genotyping array and the first 20 principal components derived from genotype data as covariates. See the Supplementary Material for extended details. In order to identify independently-associated variants (“index variants”), clump-based pruning was applied in FUMA using an r2 of 0.1 and a 1 Mb sliding window using the UKB White British sample as the LD reference panel. A 1 Mb window was used due to the regions of extended linkage disequilibrium on chromosomes 4q23 and 17q21.31, which were associated with AUDIT scores in this study.
