Our approach to identify human disease-associated SNPs amongst the 2,596 top cerebellar eGWAS cisSNPs may be overly conservative, given our selection criteria to only include transcripts that are detectable in >75% of the subjects and only those cisSNPs that are significant in both independent cohorts (ADs and non–ADs). Furthermore, given that our eGWAS genotyping platform consisted of ∼300 K SNPs, it is plausible that transcript associations with SNPs from the “Catalog of Published GWAS” [26] may be missed if those SNPs did not exist in our platform. To address these issues, we repeated the cerebellar and temporal cortex eGWAS, without restrictions for transcript detection rates and using genotypes imputed to HapMap2 (>2 million SNPs). Comparison of the eGWAS associations with p<1.0E-4 to the “Catalog of Published GWAS” identified 392 unique cerebellar cisSNPs that also associate with 189 human diseases/traits; and 339 such temporal cortex cisSNPs associating with 167 diseases/traits (Text S1, Supplementary Tables 10 and 11 in Dataset S1). Amongst the associations identified by this less stringent approach were those for brain levels of CLU [39], [40], CR1 [40] and GAB2 [41] which were identified as risk loci in GWAS of Alzheimer's disease.
