Estimated haplotype frequencies defined by the three frequent SNPs in the FOXC2 gene

SNPs −512 −350 +1548Control subjects (n = 200)Type 2 diabetic subjects (n = 195)
C   G - C0.4470.456
T   G - C0.3230.303
C   T - C0.1300.136
C   G - T0.1000.105
Total frequency1.0001.000
  • Haplotype frequencies between three SNPs were estimated based on the Arlequin program (16). The frequencies of four major haplotypes are shown. The frequencies of the other four minor haplotypes were <10−5. When the linkage disequilibrium was analyzed using the likelihood ratio test in EH program (15), linkage disequilibrium was apparent in each group (χ2 = 46.0, P = 2.43 × 10−9 in control subjects and χ2 = 45.6, P = 2.94 × 10−9 in type 2 diabetic subjects). 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.