Table 2.
Description of the variants with predicted high, moderate, or modifier impact, and new variants for the genes ABO, CCR9, CXCR6, FYCO1, LZTFL1, and SLC6A20.
| Gene | Position | SNP ID | Ref a | Var b | Impact Predicted by SnpEff | Variant Allele Frequency | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| NAM | AFR | AMR | EAS | EUR | SAS | ||||||
| ABO | 133256189 | rs55727303 | C | T | High | 0.281 | 0.001 | 0.108 | - | 0.012 | 0.026 |
| ABO | 133255902 | rs8176748 | C | T | Moderate | 0.814 | 0.243 | 0.431 | 0.290 | 0.221 | 0.220 |
| ABO | 133256085 | rs8176740 | A | T | Moderate | 0.814 | 0.242 | 0.431 | 0.289 | 0.221 | 0.220 |
| ABO | 133256264 | rs1053878 | G | A | Moderate | 0.016 | 0.256 | 0.068 | 0.151 | 0.099 | 0.029 |
| ABO | 133257465 | rs8176721 | G | A | Moderate | 0.000 | 0.155 | 0.017 | - | 0.005 | - |
| ABO | 133257486 | rs8176720 | T | C | Moderate | 0.814 | 0.489 | 0.494 | 0.483 | 0.337 | 0.464 |
| ABO | 133257246 | rs2073824 | A | G | Modifier | 0.728 | 0.469 | 0.496 | 0.549 | 0.336 | 0.465 |
| ABO | 133257320 | rs2073825 | A | T | Modifier | 0.235 | 0.241 | 0.431 | 0.289 | 0.222 | 0.225 |
| ABO | 133262062 | * | C | A | Modifier | 0.016 | - | - | - | - | - |
| ABO | 133275050 | rs616154 | C | T | Modifier | 0.031 | 0.531 | 0.408 | 0.408 | 0.535 | 0.631 |
| ABO | 133275068 | rs559723 | A | G | Modifier | 0.184 | 0.531 | 0.408 | 0.408 | 0.536 | 0.631 |
| CCR9 | 45894830 | rs7648467 | C | A | Modifier | 0.014 | 0.448 | 0.050 | - | 0.013 | 0.008 |
| CCR9 | 45897524 | rs17764980 | G | A | Modifier | 0.000 | 0.005 | 0.058 | 0.004 | 0.120 | 0.383 |
| CXCR6 | 45946488 | rs2234355 | G | A | Moderate | 0.033 | 0.491 | 0.068 | - | 0.005 | 0.001 |
| FYCO1 | 45959401 | * | G | A | Low | 0.019 | - | - | - | - | - |
| FYCO1 | 45923752 | rs35678722 | G | A | Moderate | 0.083 | 0.012 | 0.001 | - | - | - |
| FYCO1 | 45966331 | rs13079478 | G | T | Moderate | 0.070 | 0.005 | 0.059 | 0.004 | 0.122 | 0.360 |
| FYCO1 | 45966333 | rs13059238 | T | C | Moderate | 0.070 | 0.019 | 0.063 | 0.004 | 0.123 | 0.359 |
| FYCO1 | 45966722 | rs113517878 | C | T | Moderate | 0.083 | 0.003 | 0.003 | - | - | - |
| FYCO1 | 45967298 | rs3796375 | G | A | Moderate | 0.822 | 0.093 | 0.565 | 0.661 | 0.431 | 0.372 |
| FYCO1 | 45967995 | rs33910087 | G | A | Moderate | 0.070 | 0.017 | 0.059 | 0.005 | 0.122 | 0.359 |
| FYCO1 | 45968372 | rs3733100 | C | G | Moderate | 0.885 | 0.210 | 0.643 | 0.667 | 0.556 | 0.731 |
| FYCO1 | 45968585 | rs4683158 | C | T | Moderate | 0.994 | 0.982 | 0.914 | 1.000 | 0.801 | 0.922 |
| FYCO1 | 45979767 | rs1306733846 | C | T | Moderate | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| FYCO1 | 45923467 | rs6800954 | C | T | Modifier | 0.143 | 0.287 | 0.193 | 0.307 | 0.216 | 0.148 |
| FYCO1 | 45936407 | rs1873002 | T | C | Modifier | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
| FYCO1 | 45938385 | rs9875616 | G | A | Modifier | 0.859 | 0.914 | 0.850 | 0.954 | 0.746 | 0.879 |
| FYCO1 | 45959378 | rs13069079 | G | A | Modifier | 0.000 | 0.005 | 0.058 | 0.004 | 0.121 | 0.371 |
| FYCO1 | 45959571 | rs1532071 | G | A | Modifier | 0.908 | 0.260 | 0.614 | 0.652 | 0.529 | 0.732 |
| FYCO1 | 45959735 | rs76597151 | G | A | Modifier | 0.014 | 0.017 | 0.062 | 0.004 | 0.122 | 0.371 |
| FYCO1 | 45969944 | rs17214952 | A | G | Modifier | 0.014 | 0.019 | 0.063 | 0.004 | 0.123 | 0.360 |
| FYCO1 | 45973053 | rs41289622 | T | G | Modifier | 0.070 | 0.005 | 0.059 | 0.004 | 0.122 | 0.361 |
| FYCO1 | 45975359 | rs751552 | A | T | Modifier | 0.814 | 0.063 | 0.565 | 0.661 | 0.431 | 0.371 |
| FYCO1 | 45981341 | rs36122610 | G | A | Modifier | 0.054 | 0.005 | 0.059 | 0.004 | 0.122 | 0.358 |
| FYCO1 | 45984767 | rs3733097 | G | A | Modifier | 0.853 | 0.067 | 0.561 | 0.655 | 0.432 | 0.372 |
| LZTFL1 | 45828480 | rs1129183 | C | T | Moderate | 0.000 | 0.043 | 0.038 | 0.039 | 0.074 | 0.077 |
| LZTFL1 | 45827235 | * | TCTG | T | Modifier | 0.016 | - | - | - | - | - |
| LZTFL1 | 45842023 | rs138230559 | C | T | Modifier | 0.009 | 0.033 | - | - | - | - |
| LZTFL1 | 45842083 | rs141398338 | A | C | Modifier | 0.083 | 0.005 | - | - | 0.002 | - |
| SLC6A20 | 45759079 | rs140440513 | C | T | Moderate | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| SLC6A20 | 45759901 | rs61731475 | T | C | Moderate | 0.000 | - | 0.006 | - | 0.014 | - |
| SLC6A20 | 45772602 | rs17279437 | G | A | Moderate | 0.017 | 0.005 | 0.043 | 0.006 | 0.092 | 0.031 |
| SLC6A20 | 45775922 | rs139429025 | T | C | Moderate | 0.000 | 0.012 | - | - | - | - |
| SLC6A20 | 45758379 | rs2251347 | C | T | Modifier | 0.994 | 0.990 | 0.976 | 0.921 | 0.954 | 0.972 |
| SLC6A20 | 45760066 | rs116638840 | C | T | Modifier | 0.027 | 0.076 | 0.010 | - | - | 0.003 |
| SLC6A20 | 45762899 | rs2191027 | C | T | Modifier | 0.014 | 0.020 | 0.193 | 0.017 | 0.299 | 0.149 |
| SLC6A20 | 45780132 | rs2252547 | T | C | Modifier | 0.155 | 0.465 | 0.614 | 0.450 | 0.591 | 0.516 |
a Reference allele; b variant allele; * variants without described SNP; (-) no annotation; NAM: Amazonian Native American populations; AFR: African populations; AMR: American populations; EAS: East Asian populations; EUR: European populations; SAS: South Asian populations. All variants described in this table follow the selection criteria based on the impact prediction of modifier, moderate, or high, according to SnpEff.