In a large eQTL study on 773 brain samples from ∼400 autopsied subjects, we demonstrate significant contribution of genetic factors to human brain gene expression, reliably detected across different brain regions and pathologies. There is significant enrichment of brain cisSNPs amongst disease-associated variants, advocating gene expression changes as a mechanism for the first time for certain genes implicated in human diseases, including PSP (SLCO1A2), PD (MMRN1), Paget's disease (OPTN) while replicating others (e.g. PD/MAPT, SLE/UC/IRF5). MAPT cisSNPs associating with PSP, PD and AD risk highlight potential common mechanisms for these neurodegenerative diseases.
