We found substantial, significant GABRG1 haplotype and SNP associations with AUD in two independent populations. The ten SNPs that showed significant associations with AUD were in approximate allelic identity in both populations (non-alcoholics: Plains Indians, MAF = 0.40 – 0.46; Finns, MAF = 0.35 – 0.50) suggesting selection pressure. In the Plains Indians the significant SNP associations were located within the one haplotype block in which GABRG1 (excluding the promoter region) is located. However in the Finns nearly all the SNPs were associated with AUD in a region that extended from the distal intergenic region, across GABRG1 and up to the GABRA2 haplotype block. This suggests that the functional locus may be found within a long-distance haplotype. Moreover, the examination of more population isolates might help to narrow down the genomic interval in which the functional variant(s) resides.
