Of the 16,820 genes tested, we identified 2,570 (15%; 1,437 of which were protein-coding) unique differentially expressed genes (DEGs) based on global ancestry variation (local false sign rate (LFSR) < 0.05; Fig. 2a, Supplementary Table 1 and Supplementary Data 1) across the caudate nucleus (n = 1,273 DEGs), dentate gyrus (n = 997), DLPFC (n = 1,075) and hippocampus (n = 1,025). While this number increased when we examined local ancestry (9,906 (62% of genes tested); 6,982 protein-coding genes; Supplementary Table 2) across the caudate nucleus (n = 6,657 DEGs), dentate gyrus (n = 4,154), DLPFC (n = 6,148) and hippocampus (n = 7,006), effect sizes between global-ancestry and local-ancestry DEGs showed significant positive correlations (all Spearman rho > 0.57, P < 0.01; Supplementary Fig. 3) across all brain regions. When examining isoform-level associations (transcripts, exons and junctions), we found an additional 8,012 unique global ancestry-associated DEGs (LFSR < 0.05; Supplementary Fig. 2, Supplementary Table 1 and Supplementary Data 1) and 6,629 unique local ancestry-associated DEGs (LFSR < 0.05; Supplementary Table 2 and Supplementary Data 2) in these BAs. Similarly,
