We used the cerebellar eGWAS as the discovery analysis and the temporal cortex eGWAS as the validation; since our goal is to identify significant cisSNP associations while minimizing any confounding factors due to pathology and given the fact that half of our subjects had pathologic AD, in which cerebellum is relatively unaffected whereas temporal cortex is one of the first affected brain regions. Nonetheless, we have also used temporal cortex as the discovery set and cerebellum as the validation, with remarkably similar results (Text S1, Supplementary Tables 7 and 8 in Dataset S1).
