Table 2. Haplotype transmission disequilibrium results within each LD block for MET haplotypesa and for the haplotype combinations from Haploview, selected by Tagger.
| LD block/SNPs | Haplotype | TR | NT | OR | (95% CI) | P-value |
|---|---|---|---|---|---|---|
| 1st block (3 SNP haplotype) | CCA | 5 | 6 | 0.83 | (0.31, 2.23) | 1.000 |
| rs38833–rs1858830–rs40238 | CCC | 47 | 44 | 1.07 | (0.76, 1.51) | 0.834 |
| CGC | 41 | 35 | 1.17 | (0.80, 1.71) | 0.567 | |
| TCA | 12 | 20 | 0.60 | (0.33, 1.08) | 0.215 | |
| 2nd block (5 SNP haplotype) | AAGCG | 151 | 154 | 0.98 | (0.81, 1.18) | 0.909 |
| rs38845–rs9641562–rs10487353–rs38846–rs12535996 | AAGTG | 199 | 148 | 1.34 | (1.13, 1.61) | 0.007 |
| GAGTG | 207 | 238 | 0.87 | (0.74, 1.02) | 0.155 | |
| GCTTA | 41 | 54 | 0.76 | (0.54, 1.07) | 0.218 | |
| 3rd block (13 SNP haplotype) | CCCTGAAGCAACT | 14 | 27 | 0.52 | (0.30–0.88) | 0.060 |
| rs39748–rs2299433–rs38849–rs722134–rs38850– | CCCTGCAACAACT | 9 | 7 | 1.29 | (0.57, 2.96) | 0.804 |
| rs2237711–rs2237712–rs11762213–rs35776110– | CCCTGCAGCAACT | 30 | 22 | 1.36 | (0.86, 2.17) | 0.332 |
| rs33917957–rs2299436–rs38854–rs38857 | CTGTGCAGCAGCC | 30 | 35 | 0.86 | (0.57, 1.29) | 0.620 |
| CTGTGCAGCAGCT | 10 | 7 | 1.43 | (0.64, 3.24) | 0.629 | |
| GCGCACAGCAATC | 29 | 21 | 1.38 | (0.87, 2.22) | 0.322 | |
| GCGTACAGCAATC | 29 | 32 | 0.91 | (0.59, 1.38) | 0.798 | |
| GCGTGCAGCAATC | 27 | 25 | 1.08 | (0.68, 1.70) | 0.890 | |
| 4th block (10 SNP haplotype) rs38859–rs10215153–rs2237717–rs34589476– rs2299440–rs17526983–rs3807997–rs2402118– rs193687–rs41736 | CACCCGCCCC | 48 | 39 | 1.23 | (0.86, 1.76) | 0.391 |
| CACCCGCCTC | 9 | 10 | 0.90 | (0.42, 1.91) | 1.000 | |
| CGCCCGCCCC | 6 | 12 | 0.50 | (0.22, 1.11) | 0.238 | |
| CGCCTGACCC | 33 | 25 | 1.32 | (0.86, 2.05) | 0.358 | |
| TGTCCACACT | 12 | 18 | 0.67 | (0.36, 1.22) | 0.362 | |
| TGTCCGCACT | 34 | 33 | 1.03 | (0.69, 1.54) | 1.000 | |
| TGTCCGCCCT | 13 | 15 | 0.87 | (0.46, 1.61) | 0.851 |
| Haplotype combinations selected by Tagger | Tagged SNP | Haplotype | TR | NT | OR | (95% CI) | P-value |
|---|---|---|---|---|---|---|---|
| rs38845, rs38846, rs38849 | rs39747 | ATG | 198 | 149 | 1.33 | (1.11, 1.59) | 0.010 |
| rs10215153, rs38859, rs38854 | rs10243024 | GCC | 66 | 54 | 1.22 | (0.90, 1.65) | 0.320 |
| rs38854, rs38849, rs2237717 | rs7798983, rs2237710 | CGC | 80 | 68 | 1.18 | (0.90, 1.65 ) | 0.370 |
| rs2299440, rs2237717, rs3807997 | rs1621, rs41741 | CCC | 64 | 60 | 1.07 | (0.79, 1.43) | 0.788 |
| rs2299436, rs9641562 | rs17138943, rs12539654, rs17138948 | GC | 68 | 75 | 0.91 | (0.69, 1.19) | 0.616 |
Abbreviations: CI, confidence interval; LD, linkage disequilibrium; NT, non-transmitted; OR, odds ratio; SNP, single nucleotide polymorphism; TR, transmitted.
a
Haplotypes only reported if there are more than 10 informative transmissions in total.
Significant results are shown in bold.