One potential mechanism by which variants could affect gene expression is by affecting RNA stability. Here, we identified 296 SNPs that were weakly associated with alcohol dependence and related traits (P values ≤ 0.001) in the meta-analyses of African American and European American samples in COGA (Lai et al., 2019a, Lai et al., 2019b, Wetherill et al., 2019) and that reside in the 3’UTR of a gene. We tested these in a high-throughput, parallel assay, PASSPORT-seq (Ipe et al., 2018, Rao et al., 2019). Most of the SNPs tested (58%) affected gene expression (FDR ≤ 0.20), and most of those lie within binding sites of RNA binding proteins and microRNAs (67% and 74%, respectively; Table 2). Just over half lie in known eQTLs for the genes they reside within. The overlap between differential expression and these known regulatory sites reinforces our findings.
