Next, we reexamined functional enrichment of ancestry-associated DEGs after removing the MHC region (that is, HLA-specific genes, MHC region and extended MHC region) to determine if the MHC region drove enrichment of immune-related pathways. After excluding the HLA genes, we still observed strong enrichment of immune-related pathways (Supplementary Fig. 17). Similarly, excluding the MHC (Supplementary Fig. 18) and the extended MHC region (Supplementary Fig. 19) also showed immune-related enrichment across brain regions. This pattern held for local ancestry DEGs (Supplementary Fig. 20), suggesting that the extended MHC region does not drive ancestry-associated DEG enrichment of immune-related pathways.
