Transmission test for linkage disequilibrium for l-histidine decarboxylase variation tSNPs and haplotypes
| Rs# | Over-transmitted allele | T:U | χ2 | p Value | Permutation p value |
|---|---|---|---|---|---|
| rs854150 | G | 284 : 220 | 8.127 | 0.0044 | 0.0290 |
| rs854151 | G | 205 : 190 | 0.57 | 0.4504 | |
| rs2070596 | T | 192 : 154 | 4.173 | 0.0411 | 0.2640 |
| rs2070595 | G | 232 : 224 | 0.14 | 0.7079 | |
| rs2853766 | A | 215 : 174 | 4.321 | 0.0376 | 0.2370 |
| rs1894236 | C | 201 : 143 | 9.779 | 0.0018 | 0.0150 |
| rs854157 | T | 277 : 245 | 1.962 | 0.1613 | |
| rs7182203 | G | 217 : 215 | 0.009 | 0.9233 | |
| rs854158 | G | 246 : 216 | 1.948 | 0.1628 | |
| rs854163 | A | 223 : 188 | 2.981 | 0.0843 | |
| rs9920021 | A | 227 : 198 | 1.979 | 0.1595 | |
| rs1365503 | A | 249 : 223 | 1.432 | 0.2314 | |
| Haplotype | Frequency | T : U | χ2 | p Value | Permutation p value |
| Block 1 | |||||
| CA | 0.620 | 224.5 : 286.7 | 7.56 | 0.006 | 0.0140 |
| GG | 0.268 | 227.2 : 195.0 | 2.465 | 0.1164 | |
| GA | 0.107 | 123.3 : 87.1 | 6.212 | 0.0127 | 0.0440 |
| Block 2 | |||||
| TGGC | 0.387 | 243.0 : 273.2 | 1.761 | 0.1845 | |
| TGAC | 0.248 | 218.0 : 173.0 | 5.179 | 0.0229 | 0.0790 |
| ATGT | 0.216 | 151.0 : 198.9 | 6.561 | 0.0104 | 0.0420 |
| TTGC | 0.140 | 147.5 : 122.3 | 2.346 | 0.1256 | |
The studied sample consists of 520 TS nuclear families of Greek, Albanian, Italian, Hungarian, Polish, Spanish, German and Canadian origin. The permutation p value was computed after 1000 permutations of the datasets. Results for the associated haplotype blocks 1 and 2 are shown (figure 1, block 1:SNPs rs854150-rs854151; block 2:SNPs rs2070596-rs2070595-rs2853766-rs1894236).
Statistically significant signals (permutation p-value lower than 0.05) are shown in bold.
T:U, transmitted–untransmitted; tSNP, tagging SNP.