Of the SNPs nominally associated with alcohol dependence diagnosis at p<.0001 in family based analyses (Table S10 in the Supplement), four also showed association in case-population control comparisons (rs1541918, Chr5, p=7.4E-6; CPC OR=1.23 (95% CI 1.06–1.42), p=.007; rs10089021, Chr8, p=4.3E-5, CPC OR=0.82 (0.77–0.94), p=.003; rs786870, Chr10, p=8.4E-5, CPC OR =0.81 (0.71–0.02), p<.001; rs2789686, Chr10, p=3.8E-5, CPC OR=0.76 (0.64–9.90), p<.001). Only one of the 29 SNPs associated with alcohol dependence at p<.0001 also shows association with HOD, the intergenic chromosome 12 SNP rs2463107 SNP that is in moderate LD with intronic SNPs in the PAWR and SYT1 genes. This SNP also shows predicted case-population control differences (OR=0.62, 95%CI 0.49–0.79, p=7E-5).
