To ensure that we did not miss any associations due to the stringent eGWAS criteria that we applied, we repeated the analyses using no restrictions for transcript detection rates and eGWAS p value threshold of p<1.0E-4. We also investigated cisSNPs identified in AD and non–AD brains, both separately, and jointly, given that some cisSNP associations may be unique to one group. We compared these eGWAS results to the ADGC GWAS as described above (Supplementary Tables 21, 22, 23, 24, 25, 26 in Dataset S1). Using cerebellar and temporal cortex eGWAS from all subjects, 561 and 488 unique transcripts with cisSNPs that yield suggestive AD risk associations were identified, respectively. There were 259–312 such transcripts identified in each AD or non–AD eGWAS, with >50% overlap between the two diagnostic groups' results, although many of these results could be identified in the eGWAS of combined samples. About 7–10% of the transcripts could only be identified in just ADs or non–ADs, but not the combined eGWAS. Amongst such unique transcripts were CLU and BIN1, which reside at the LOAD GWAS loci [39], [40],
