The ancestry-specific GWAS analyses revealed no genome-wide significant associations (P<5x10-8, S3 and S4 Figs.). To identify SNP/indel associations with HIV acquisition that are shared across the ancestral groups, we conducted a GWAS meta-analysis of AA and EA IDUs in the UHS cohort based on 8 million imputed SNP and indel genotypes (MAF > 0.5%). The resulting quantile-quantile plot showed some deviation from expectation among top SNP/indel associations but no genomic inflation (λgc = 1.008; S5 Fig.). We identified one genome-wide significant association on chromosome 19 upstream of the CD33 gene (rs3987765 meta-analysis p = 4.38x10-8) and 6 other regions of interest (P<1x10-6). An eighth region on chromosome 9 had the top genotyped SNP association (P = 1.02x10-5). The 692 SNPs and indels selected for replication testing from the 8 regions are highlighted in Fig. 2. Their regional association plots from the GWAS meta-analysis are shown in S6 and S7 Figs.
