LDSC27 was used to calculate population-specific LD scores based on 1000 Genomes phase 3 datasets according to the LDSC tutorial, using SNPs selected from HapMap 3 (ref. 50) after excluding the major histocompatibility complex (MHC) region (chr6: 26–34Mb); only ancestry groups with large sample size (N > 10,000) were analyzed using LDSC. Of note, LDSC could be biased in admixed populations because reference panels are not provided for AAs and LAs in that application27. We calculated LD scores for 1,215,001 SNPs in EAs; 1,322,841 SNPs in AAs; and 1,243,726 SNPs in LAs. The LDSC analyses used SNPs with imputation INFO ≥ 0.9 in each population and that were LD scored in 1000 Genomes. LD score regression intercepts for available datasets were estimated to distinguish polygenic heritability from inflation. SNP-based heritability (h2 SNP) was estimated from GWAS summary statistics for both AUDIT-C and AUD. The sex-specific h2 SNP was also estimated in EA males and females, AA males, and LA males.
