To achieve internal replication, we first analyzed the ADs and non–ADs separately. In our cerebellar eGWAS, at q<0.05, there were 5,271 significant cisSNP/transcript associations (1,156 unique genes) in the AD, 4,450 (1,022 unique genes) in the non–AD and 10,281 (1,875 unique genes) in the combined datasets. Q-Q plots suggested a clear excess of significant results (Figure 1, Figure S1a–S1d). 2,980 cisSNP/transcript associations (2,596 unique cisSNPs, 686 unique genes) were significant at q<0.05 in both ADs and non–ADs (Table 1, Supplementary Table 3 in Dataset S1, Figure S2). The direction and magnitude of associations in both groups demonstrate remarkable similarities (Pearson's correlation coefficient = 0.98, p<0.0001). The box plots depicted for some of these top associations (Figure S3a–S3c) demonstrate this replication in ADs and non–ADs. Most associations have an additive or dominant pattern with respect to the minor allele.
