Linkage disequilibrium between two of the three SNPs in the FOXC2 gene and haplotype frequencies in control subjects

HaplotypeEstimated HFExpected HFDD′χ2P
−512 +154821.2<10−5
 C - C0.5770.610−0.033−1
 C - T0.1000.067+0.033+1
 T - C0.3230.290+0.033+1
 T - T0.0000.033−0.033−1
−512 −35028.5<10−7
 C - G0.5470.589−0.042−1
 C - T0.1300.088+0.042+1
 T - G0.3230.281+0.042+1
 T - T0.0000.042−0.042−1
−350 +15485.500.019
 G - C0.7710.783−0.012−0.917
 G - T0.0990.087+0.012+0.917
 T - C0.1290.117+0.012+0.917
 T - T0.0010.013−0.012−0.917
  • To examine a deviation from linkage equilibrium between 2 SNPs, a χ2 test was performed as described by Imanishi et al. (18). The nucleotide number of each SNP is counted from A of the start codon as 1, with the caution that the one base shorter numbers than those from the human draft sequence for the FOXC2 gene are used beyond +1060 as correct reference numbers. HF, haplotype frequency; D, linkage disequilibrium parameter; D′, relative linkage disequilibrium value.