TABLE 2

Haplotype analysis of six-SNP HNF4A haplotypes in type 2 diabetic ESRD subjects vs. control subjects using HAPLO.SCORE (25) and Dandelion (26)

HaplotypeCase subject frequency (%)Control subject frequency (%)Hap scoreEmpirical Hap-specific P valueGlobal simulated P value
Six SNPs in strongest LD block (rs2868093, rs4810424, rs1884613, rs1884614, rs2144908, rs6073418)
    TCGTAC9.613.2−1.880.053
    CGCCGT30.835.8−1.50.13
    CCGTAC2.83.3−0.040.95
    CGCCGC47.846.30.290.78
    TCCTAC2.403.280.0003
    CGGCGT2.203.811.00E-062.00E-06
Six SNPs in second LD block (rs1885088, rs1885089, rs3212198, rs1028583, rs1028584, rs2273618)
    GCTTAC0.36.8−4.26<0.0001
    GCCGCT05.0−3.92<0.0001
    GCCGCC2.22.3−0.010.99
    ATTGCC20.220.20.010.99
    GCTGCC34.929.91.320.19
    GCCTAT40.132.41.970.05<0.0001