To understand one potential mechanism of action underlying loci associated with AD and related phenotypes, we selected 296 SNPs that showed some evidence of association (p ≤ 0.001) and were located in 3’UTRs, and simultaneously tested whether they affected gene expression using a high-throughput assay, PASSPORT-seq (Rao et al., 2019). Both alleles of 84% and 86% of the SNPs were detected in both DNA and RNA in every replicate in SH-SY5Y and SK-N-BE(2) cells, respectively (Supplementary Table S3). We identified 60 SNPs (FDR < 0.05) that affected gene expression in the SH-SY5Y and 92 in SK-N-BE(2) cells (Table 1) Among these, 30 SNPs altered the RNA levels relative to DNA levels in the same direction in both cell lines (Figure 1A; Table 2); this degree of overlap is significant (Fisher’s exact test, p = 4.91 × 10−7). The alternative allele frequency of RNA vs DNA and the read depth for four representative SNPs with significant differential expression in both cell lines are shown in Figure 1B. Relaxing the FDR to < 0.2, there were 102 functional SNPs in SH-SY5Y and
