As yet, there is no known functional locus in either GABRA2 or GABRG1. Although GABRA2 has four common isoforms (Tian et al, 2005) GABRG1 has no known isoforms. There is a microRNA binding site in the GABRG1 3′ UTR, however no SNPs overlap with that site. The fact that the chr 4 genes cluster together and that there is extensive LD across the cluster suggests the presence of distant enhancers and repressors. Using NCBI and HapMap we determined that the nearest gene, GNPDA2 (glucosamine-6-phosphate deaminase 2), is at a distance of more than 1 Mb and several major haplotype blocks downstream from GABRG1. Moreover, long-distance LD does not extend downstream from the GABRG1 haplotype block. Therefore it seems likely that the functional locus is located in the, admittedly extensive, region covered by the extended haplotypes. We used HapMap haplotypes for the Caucasian, Asian and African samples to determine the two major ancestral GABRG1 haplotypes (H1 and H3 + H4 as shown in Figure 5) and created the haplotype specific sequences from NCBI refGene’s GABRG1 transcript (NM_173536.3). We ran Mfold 3.2
