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Chunk #5 — Materials and Methods — Selection of 3’UTR SNPs

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Identification of Functional Genetic Variants Associated With Alcohol Dependence and Related Phenotypes Using a High-Throughput Assay.
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et al., 2019a, Lai et al., 2019b). GWAS of 11 phenotypes in the COGA African American (AA) and European American (EA) samples, as well as meta-analyses of them have been published (Lai et al., 2019a, Lai et al., 2019b, Wetherill et al., 2019). For the current study, we performed GWAS for another seven alcohol related phenotypes, making 18 GWAS in total (Supplemental Table S1). We then selected for PASSPORT-seq analysis 296 variants that are located in the 3’ UTR of genes (defined by NCBI RefSeq annotation) and had P-values ≤ 0.001 in any of those GWAS. An advantage of high-throughput assays is the ability to test many SNPs that are not genome-wide significant in current underpowered GWAS but might be functional and thereby potentially contribute to the risk for the disorder. The list of 296 SNPs used in this study is in Supplemental Table S2.