In order to determine the haplotype block structure across the 493 kb GABRG1 and GABRA2 region, 10 GABRA2 SNPs from the Illumina Linkage IV-B panel, previously genotyped with the Illumina GoldenGate platform under contract at Illumina (Hodgkinson et al, 2008), were included in the analyses. In addition, two previously genotyped GABRA2 SNPs (rs279863 and rs279858) (Enoch et al, 2006a) that tagged the two common GABRA2 yin-yang haplotypes, were included. These two SNPs, particularly rs279858, have been most strongly associated with alcohol dependence in earlier studies. The inclusion of these two SNP allows for cross comparison with earlier studies. The genotyped GABRA2 SNPs were (5′ to 3′): rs11503014; haplotype block 1: rs9291283, rs1442060; haplotype block 2: rs10805145, rs426463, rs279827, rs279843, rs279847, rs279858, rs279863, rs519270 and rs693547.
