for rs3752462, with very high LD (r2>0.9). Therefore we also measured frequencies and associations for haplotype E-1p, which is defined by the risk alleles for SNP rs4821481 and rs8141971, and for haplotype T-1, defined by the risk alleles for SNP rs2239785 and SNP rs136187. We picked these two SNPs as they were found to be the best predictor for the disease among all possible pair of SNPs from Table 2. Interestingly, these SNPs are in significant linkage disequilibrium in African Yoruba samples from Hapmap (D′=0.43, r2=0.07) while almost in complete linkage equilibrium in European samples from Hapmap (D′=0.12, r2=0.002). We performed the haplotype analysis using Plink.
