SAGE). Family structures were updated, as needed. Using genetically-confirmed pedigrees, Pedcheck (O’Connell & Weeks, 1998) was used to identify Mendelian errors and inconsistencies were removed. The same set of variants were used to estimate PCs using Eigenstrat (Price et al., 2006) with 1000 Genomes data serving as the reference (Phase 3, version 5). Only AA samples, designated based on the first two PCs (COGA N=2,939; SAGE N=959; Yale-Penn N=2,044; NIAAA N=169), were included in analyses (Lai, Wetherill, Bertelsen, et al., 2019; Lai, Wetherill, Kapoor, et al., 2019). For the purposes of fine mapping, all samples were imputed to 1000 Genomes (Phase 3, version 5, hg19) separately by cohort using SHAPEIT2 (Delaneau, Howie, Cox, Zagury, & Marchini, 2013) followed by Minimac3 (Das et al., 2016). Only variants with non A/T or C/G alleles, missing rates <5%, MAF >3%, and HWE P-values >0.0001 were used for imputation. Imputed variants with imputation quality score R2 <0.30 were excluded.
