Despite the assumption that brain eQTLs would also influence human diseases and traits, there are no systematic gene mapping studies for human diseases that utilize brain gene expression phenotypes. Furthermore, the brain region most relevant for such studies and the influence of brain pathology on eQTL mapping studies are largely unknown. To address these issues, we performed an eQTL using cerebellar tissue from 197 subjects with Alzheimer's disease (AD) neuropathology and 177 with other pathologies (non–AD). We validated the results in a different brain region using temporal cortex samples from 202 ADs and 197 non–ADs (Supplementary Tables 1 and 2 in Dataset S1), 85% of whom overlapped with the cerebellar group. We evaluated significant cisSNPs from our study for association with human diseases/traits using a GWAS catalog [26]. We also assessed our significant eGWAS cisSNPs for association with two central nervous system (CNS) diseases, progressive supranuclear palsy (PSP) [27] and AD risk [28], using two recent GWAS for these diseases.
