The most common of the three ancestral, extended haplotypes was associated with AUD in both populations; the other two ancestral haplotypes (identical except for the GABRA2 contribution) were more abundant in non-alcoholics. Our results suggest that the signal for the extended haplotypes’ association with AUD derives from GABRG1 and is independent of GABRA2 (Figure 5). However the differential impact of GABRA2 haplotypes was observed in the less common (< 0.05 frequency) long distance haplotypes. We had noted that in both samples, two GABRG1 SNPs: rs13130508 and rs10517150 (not associated with AUD), showed exceptionally high LD (D′ = 0.9 – 1.0) with GABRA2 SNPs indicating the likelihood that they are located in ancient chromosomal regions. However, the variant alleles of these two SNPs were not embedded in the three common ancestral haplotypes described above. Instead, in the Finns they were found in three haplotypes that differed only in the GABRA2 haplotype contribution and it was these GABRA2 haplotypes that determined the haplotype association with AUD. These three ancestral haplotypes account for only 0.06 of the extended haplotype diversity and therefore they
