GABRA2 contains two large haplotype blocks, and a synonymous SNP in the exon of the GABRA2 gene, rs279858, tags a haplotype that is correlated with severity of alcoholism and is itself associated with heavy drinking (Enoch, 2008). This SNP was not on the Illumina array but could be imputed successfully (with an r2 of .960), and the risk allele, G, was associated with reduced beta power in our sample, t = −2.46, p = .014. To assess the degree to which there might be an additional signal in GABRA2, we repeated our analysis of imputed SNPs, this time including each individual’s dosage for rs279858 as a covariate. Adjusting for this SNP substantially reduced the magnitude of associations between the other SNPs in the gene and beta power, presented graphically in the bottom panel of Figure 15. rs511310, which previously had yielded the smallest p-value and which is not in strong LD with the other SNPs (median across all SNPs in the gene, 0.09) remained the SNP with the strongest effect.
