Observing immune response pathway enrichment in bulk tissue, we performed cell type23,24 enrichment analysis to evaluate the cellular context of these ancestry-associated DEGs. We found significant enrichment of global ancestry DEGs (Fisher’s exact test, FDR < 0.05; Supplementary Figs. 10 and 11a) for genes specifically expressed in brain immune cells (that is, glia and microglia) and neurovasculature cells (that is, pericyte, endothelial and vascular tissue), but not peripheral immune cells. We also observed enrichment for distinct glial subtypes25 (Supplementary Fig. 12). Local ancestry-associated DEGs showed significant enrichment for brain and non-brain immune cells (Fisher’s exact test, FDR < 0.05; Supplementary Figs. 11b and 13), potentially due to the larger number of detected DEGs. Even so, we found that the level of enrichment of non-brain immune cells (global and local) on average was smaller than brain immune cells. We consistently found significant depletion of DEGs (global and local) for neuronal cell types. Moreover, we observed immune-related pathways and associated cell types (that is, microglia and perivascular macrophages) for DEGs upregulated with increasing AA proportion in the caudate nucleus and upregulated with
