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Table 2 Two-stage analysis: selected SNPs and their corresponding p-values in the second stage

From: Joint analysis of case-parents trio and unrelated case-control designs in large scale association studies

Chromosome SNP Distance (Mb) Z TDT then Z CC Z CC then Z TDT Z TDT or Z CC then Zjoint
6 SNP6_128 7.13 1.02 × 10-8   1.61 × 10-7
  SNP6_129 7.10 4.01 × 10-13   1.45 × 10-8
  SNP6_130 7.10 1.48 × 10-13   1.28 × 10-9
  SNP6_134 6.41 5.76 × 10-10   1.33 × 10-6
  SNP6_138 b 3.73 2.89 × 10 -15 2.85 × 10 -7 1.07 × 10 -13
  SNP6_139 3.72 2.44 × 10 -15 3.75 × 10 -7 1.22 × 10 -13
  SNP6_145 2.92 1.03 × 10 -9 5.20 × 10 -6 1.24 × 10 -9
  SNP6_147 2.22 1.37 × 10 -8   3.05 × 10 -7
  SNP6_150 1.39 5.99 × 10 -7   6.25 × 10 -7
  SNP6_152 c 0.04 2.38 × 10 -221 1.55 × 10 -94 4.31 × 10 -193
  SNP6_153 0.01 0*a 7.33 × 10 -206 0*a
  SNP6_154 0.04 0* 1.23 × 10 -182 0*
  SNP6_155 0.29 4.49 × 10 -87 1.91 × 10 -49 7.36 × 10 -86
  SNP6_160 0.65 8.62 × 19 -10 8.20 × 10 -9 1.16 × 10 -11
  SNP6_162 0.13 9.15 × 10 -24 1.78 × 10 -15 9.36 × 10 -26
11 SNP11_387 0.19    3.00 × 10 -6
  SNP11_389 0.03 2.78 × 10 -28 3.33 × 10 -15 2.41 × 10 -27
18 SNP18_269 0.02 2.25 × 10 -8   1.56 × 10 -8
  1. a0*, p-value < 10-300. Test statistics are based on an additive genetic model.
  2. bItalic, SNPs within 5 Mb of the major genes.
  3. cBold, SNPs within 1 Mb of the major genes.