It is not obvious whether the cisSNP that display similar effects in different brain regions and different disease types would have relevance to human disease. The top 2,596 cerebellar cisSNPs that are significant in both ADs and non–ADs, and many of which are also significant in the temporal cortex are also enriched for variants implicated in human disease, including CNS disease, such as PD and PSP. Thus, the fourth implication of our study is that it may be possible to map disease-associated variants using eQTL studies conducted in unaffected tissue or unaffected subjects. In addition to providing a general characterization of the genetics of brain gene expression, this study successfully replicated many previously published cisSNP associations, such as rs8070723/ MAPT level, rs11012/ LRRC37A4 level associations, both of which were implicated in PD. We found novel brain expression level associations for transcripts implicated in disease, including rs11568563 association with SLCO1A2, recently identified in a PSP GWAS. The disease-associating cisSNP associations identified in this study were not restricted to CNS diseases, but also included non–CNS diseases, such as SLE, where we replicated the previously published rs4728142/ IRF5 level associations.
