Linkage Disequilibrium of SNPLinkag

Linkage Disequilibrium of SNP
Linkage disequilibrium (LD) of the 5 SNP were measured by Lewontin’s D′ (|D′|) and r2 with Haploview version 4.1 software. Lewontin’s D′ (|D′|) and r2 of C4535156T and G4533815A SNP, C4535156T and G4533675C SNP, G4533815A and G4533675C SNP of the STAT5B gene were 0.939 and 0.852, 0.967 and 0.858, and 0.971 and 0.896, respectively. When r2 is higher than 0.3, two loci are considered in LD, and when r2 is higher than 0.6, two loci are considered in strongly LD (Ardlie et al., 2002). Moreover, 1 haplotype block has been defined as 3 or more markers for which all estimated values of |D′| exceeded 0.9 (Phillips et al., 2003). The results indicated that the 3 SNP of the STAT5B gene were strong-linked with each other and lay within a haplotype block; thereinto, the G4533815A SNP was tagSNP. In addition, D′ and r2 of T56039403C and C56072547T SNP of IGFBP1 and IGFBP3 genes were 0.949 and 0.465, respectively, and the 2 SNP were in LD.