The genes selected by COGA authors as being associated with alcohol phenotypes (Aliev et al., 2015) were used in the analyses. Nine of these genes were not represented by SNPs on the chip array we used for genotyping, prohibiting their inclusion in the analysis. In total, 104 genes were included. Gene locations and ranges were gathered using GRCH37.p13 coordinates from the UCSC Table Browser. These gene location ranges (and the genes that could not be included in analyses) are provided in a downloadable excel file (Supplemental Results). All available SNPs (3,281) within these coordinate ranges that passed SNP-level quality control filters (minor allele frequency > 5%, genotype missing by SNP < 2%) were included in analysis. The list of SNPs included in each analysis and their corresponding individual p-values are provided as Supplemental Results (to be found online). One SNP deviated from Hardy-Weinberg equilibrium just beyond the p < 5 × 10−5 level, which commonly occurs in studies using genome-wide data (Anderson et al., 2010; Turner et al., 2011). All other SNPs were consistent with Hardy-Weinberg equilibrium above this value. Hardy-Weinberg Statistics for every SNP tested are provided in the supplemental materials.
