TABLE 2

Haplotype analysis using HAPLO.SCORE with eight SNP (rs941798, rs3787345, rs754118, rs2282147, rs718049, rs718050, rs3787348, and 1484insG) PTPN1 haplotypes

HaplotypeHaplotype frequency in case subjectsHaplotype frequency in control subjectsOverall haplotype frequencyHAP-ScoreEmpirical HAP-specific P valueOverall P value
300 Caucasian type 2 diabetic–ESRD and 310 Caucasian control subjects
    GTCCTGTO0.410.450.43−1.870.0570.041
    ATCCTGGG0.060.090.07−2.120.028
    ACCCTGGO0.020.020.020.490.470
    ACCCCAGO0.020.020.020.180.940
    ATCCTGGO0.090.070.081.40.175
    ACTTCAGO0.390.330.362.650.009
275 Caucasian DHS–type 2 diabetic and 200 Caucasian control subjects
    GTCCTGTO0.390.470.43−2.990.00230.055
    ATCCTGGG0.070.080.08−1.910.054
    ACCCTGGO0.010.020.02−0.640.490
    ACCCCAGO0.030.020.020.250.800
    ATCCTGGO0.070.040.061.950.061
    ACTTCAGO0.410.340.372.110.033
Combined case and control populations: 575 case subjects and 510 control subjects
    GTCCTGTO0.410.460.43−2.990.0020.003
    ATCCTGGG0.070.090.08−1.910.055
    ACCCTGGO0.0130.020.02−0.630.47
    ACCCCAGO0.020.020.020.250.8
    ATCCTGGO0.080.060.072.150.03
    ACTTCAGO0.400.330.363.420.0004