We also examined eQTLs whose effects may vary based on genetic ancestry (interaction between variant and global ancestry proportion), identifying at least one ancestry-dependent cis-eQTL for 943 unique genes across brain regions (LFSR < 0.05, n = 531, 942, 573 and 531 for the caudate nucleus, dentate gyrus, DLPFC and hippocampus, respectively; Supplementary Fig. 22, Supplementary Table 4 and Supplementary Data 7). Most of these eGenes (510 (54.1%) eGenes) were shared across the four brain regions (Supplementary Fig. 23). This relatively limited detection of ancestry-dependent eQTLs supports other work showing high correlation of causal effects across local ancestry of admixed individuals31.
