To investigate whether any of the significant brain cisSNPs may influence risk of AD, we compared our eGWAS results to the AD risk associations from the large AD GWAS conducted by ADGC [28]. We obtained results of meta-analyses for the ADGC Stage 1+2 cohort (11,840 LOAD vs. 10,931 controls) [28] and investigated those SNPs with suggestive AD risk association in this dataset (pmeta<10−3). To ensure uniform comparison between our eGWAS and the ADGC GWAS, we assessed results from >2 million SNPs for each study using SNPs genome-wide imputed to HapMap phase 2 (release 22). There were 77,126 cerebellar (63,652 unique SNPs, 2,338 unique genes) and 68,172 temporal cortex (57,922 unique SNPs and 2,201 unique genes) cisSNP/transcript associations significant at q<0.05 representing a clear excess (Figure S6). There were 380 cisSNPs that were significant for the cerebellar transcript associations and also had suggestive AD risk associations (2.9-fold enrichment), 432 such temporal cortex cisSNPs (3.3-fold enrichment) and 356 cisSNPs significant in both the cerebellum and temporal cortex (2.7-fold enrichment, p<10−6 for all three analyses) (Figure 1, Supplementary Tables 19 and 20 in Dataset S1).
