The position of each of these SNPs with respect to the intron exon structure of GABRA2 and the amount of linkage disequilibrium between the markers are given in Figure 1. As the figure demonstrates, an extensive block of linkage disequilibrium extending from intron three into the intergenic region between GABRA2 and the neighboring gene, GABRG1 is present. However, linkage disequilibrium quickly decays immediately 3′ to GABRA2 exon three with only marginal linkage disequilibrium being present between the 4 most centromeric SNPs in our study. This breakdown in disequilibrium does not appear to be secondary to genotyping difficulties with each of these markers having genotyping success rates of 99.3% or greater and is consistent with prior dense haplotyping of this region [1].
