We next tested whether these eGenes (main effect and ancestry-dependent) were likely to be differentially expressed by genetic ancestry. Across brain regions, we found significant enrichment (Fisher’s exact test, FDR < 0.05) of these eGenes (LFSR < 0.05) with ancestry-associated DEGs (LFSR < 0.05; Fig. 4c and Supplementary Fig. 23c). Given the potential correlation of genotypes with eGenes and ancestry inference, we also examined allele frequency differences (AFDs) between DEGs and non-DEGs. We found a significant increase in AFDs for DEGs compared with non-DEGs (Mann–Whitney U-test, P < 0.05; Fig. 4d and Supplementary Fig. 24) across brain regions. These results suggest that a genetic component is probably influencing these expression differences, potentially because of divergence in allele frequencies.
