Table 1.
Allele distributions of cross-trial–validated associated thalidomide-related VTE SNPs
| SNP | Chromosome | Gene | Functional class | Minor allele | MAF patients | MAF controls | Major allele | P | OR | L95 | U95 | Empirical P | Trial | In Linkage |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs2302387 | 7 | ABCB4 | Coding-synon | A | 0.085 | 0.1432 | G | .042 | 0.5557 | 0.3133 | 0.9857 | .041 | Myeloma IX | |
| A | 0.375 | 0.4 | G | .879 | 0.9 | 0.2331 | 3.475 | .857 | Hovon-50 | |||||
| A | 0 | 0.18 | G | .112 | NA | NA | NA | .149 | E1A100 | |||||
| rs1049216 | 4 | CASP3 | Untranslated | C | 0.19 | 0.2891 | T | .009 | 0.5769 | 0.3804 | 0.875 | .006 | Myeloma IX | |
| C | 0.2778 | 0.4545 | T | .251 | 0.4615 | 0.1221 | 1.745 | .345 | Hovon-50 | |||||
| C | 0.08333 | 0.42 | T | .029 | 0.1255 | 0.01503 | 1.049 | .087 | E1A100 | |||||
| rs506504 | 11 | CHEK1 | Coding-nonsynon | T | 0.06633 | 0.02865 | C | .031 | 2.409 | 1.059 | 5.481 | .044 | Myeloma IX | |
| T | 0.1111 | 0 | C | .109 | NA | NA | NA | .146 | Hovon-50 | |||||
| T | 0.25 | 0.06 | C | .046 | 5.222 | 0.9057 | 30.11 | .060 | E1A100 | |||||
| rs7011 | 14 | CINP | Coding-nonsynon | T | 0.3081 | 0.2266 | C | .032 | 1.52 | 1.034 | 2.233 | .036 | Myeloma IX | |
| T | 0.3889 | 0.25 | C | .358 | 1.909 | 0.4772 | 7.638 | .357 | Hovon-50 | |||||
| T | 0.5 | 0.22 | C | .051 | 3.545 | 0.9522 | 13.2 | .096 | E1A100 | |||||
| rs12022378 | 1 | DCLRE1B | Coding-nonsynon | T | 0.2323 | 0.1536 | C | .019 | 1.667 | 1.083 | 2.565 | .023 | Myeloma IX | |
| T | 0.2222 | 0.09091 | C | .247 | 2.857 | 0.4585 | 17.8 | .632 | Hovon-50 | |||||
| T | 0.25 | 0.22 | C | .823 | 1.182 | 0.2723 | 5.13 | .999 | E1A100 | |||||
| rs4253211 | 10 | ERCC6 | Coding-nonsynon | C | 0.1616 | 0.09896 | G | .028 | 1.755 | 1.059 | 2.909 | .035 | Myeloma IX | |
| C | 0.1667 | 0.04545 | G | .204 | 4.2 | 0.3973 | 44.4 | .261 | Hovon-50 | |||||
| C | 0.1667 | 0.1 | G | .512 | 1.8 | 0.3044 | 10.64 | .560 | E1A100 | |||||
| rs299295 | 5 | HMMR | Coding-nonsynon | T | 0.28 | 0.1979 | C | .024 | 1.576 | 1.059 | 2.346 | .041 | Myeloma IX | |
| T | 0.3889 | 0.2727 | C | .435 | 1.697 | 0.4472 | 6.439 | .999 | Hovon-50 | |||||
| T | 0.3333 | 0.32 | C | .929 | 1.063 | 0.2784 | 4.055 | .999 | E1A100 | |||||
| rs582537 | 3 | IL12A | Intron | A | 0.515 | 0.3995 | C | .007 | 1.596 | 1.132 | 2.251 | .005 | Myeloma IX | rs2227314 |
| A | 0.5 | 0.5 | C | .999 | 1 | 0.2877 | 3.476 | .999 | Hovon-50 | rs2227314 | ||||
| A | 0.5833 | 0.44 | C | .372 | 1.782 | 0.4973 | 6.385 | .591 | E1A100 | rs2227314 | ||||
| rs10249476 | 7 | LEP | Promoter | T | 0.405 | 0.3115 | G | .024 | 1.504 | 1.054 | 2.147 | .026 | Myeloma IX | |
| T | 0.5556 | 0.4091 | G | .356 | 1.806 | 0.5123 | 6.363 | .450 | Hovon-50 | |||||
| T | 0.3333 | 0.2083 | G | .360 | 1.9 | 0.4743 | 7.611 | .517 | E1A100 | |||||
| rs20579 | 19 | LIG1 | Untranslated | T | 0.065 | 0.1263 | C | .022 | 0.481 | 0.2544 | 0.9094 | .017 | Myeloma IX | |
| T | 0.05556 | 0.2727 | C | .072 | 0.1569 | 0.01696 | 1.451 | .113 | Hovon-50 | |||||
| T | 0 | 0.04 | C | .481 | NA | NA | NA | .999 | E1A100 | |||||
| rs13815 | 22 | MT | Coding-nonsynon | C | 0.2576 | 0.3679 | G | .007 | 0.5961 | 0.4078 | 0.8716 | .010 | Myeloma IX | |
| C | 0.2222 | 0.4545 | G | .125 | 0.3429 | 0.08519 | 1.38 | .126 | Hovon-50 | |||||
| C | 0.25 | 0.36 | G | .470 | 0.5926 | 0.142 | 2.473 | .857 | E1A100 | |||||
| rs2410558 | 8 | NAT2 | Locus | T | 0.215 | 0.3032 | C | .024 | 0.6295 | 0.4208 | 0.9416 | .024 | Myeloma IX | |
| T | 0.2222 | 0.5 | C | .071 | 0.2857 | 0.07114 | 1.148 | .226 | Hovon-50 | |||||
| T | 0.25 | 0.28 | C | .834 | 0.8571 | 0.202 | 3.636 | .999 | E1A100 | |||||
| rs3774968 | 4 | NFKB1 | Intron | A | 0.355 | 0.4581 | G | .017 | 0.651 | 0.4575 | 0.9263 | .017 | Myeloma IX | |
| A | 0.3333 | 0.3182 | G | .919 | 1.071 | 0.2838 | 4.046 | .999 | Hovon-50 | |||||
| A | 0.4 | 0.46 | G | .728 | 0.7826 | 0.1965 | 3.117 | .800 | E1A100 | |||||
| rs1805414 | 1 | PARP1 | Coding-synon | C | 0.25 | 0.3376 | T | .029 | 0.6539 | 0.4459 | 0.9592 | .033 | Myeloma IX | rs1002153, rs2048426, rs2267669 |
| C | 0.2222 | 0.4545 | T | .125 | 0.3429 | 0.08519 | 1.38 | .328 | Hovon-50 | rs1002153, rs2048426, rs2267669 | ||||
| C | 0.3333 | 0.36 | T | .862 | 0.8889 | 0.2346 | 3.367 | .999 | E1A100 | rs1002153, rs2048426, rs2267669 | ||||
| rs2267669 | 6 | PPARD | Intron | G | 0.1198 | 0.2139 | A | .006 | 0.5001 | 0.3031 | 0.8253 | .007 | Myeloma IX | |
| G | 0 | 0.2273 | A | .031 | NA | NA | NA | .037 | Hovon-50 | |||||
| G | 0.1667 | 0.1818 | A | .903 | 0.9 | 0.1643 | 4.929 | .999 | E1A100 | |||||
| rs2070682 | 7 | SERPINE1 | Intron | C | 0.365 | 0.4562 | T | .034 | 0.6852 | 0.4827 | 0.9728 | .029 | Myeloma IX | |
| C | 0.3333 | 0.3636 | T | .842 | 0.875 | 0.2362 | 3.241 | .999 | Hovon-50 | |||||
| C | 0.4167 | 0.42 | T | .983 | 0.9864 | 0.2749 | 3.539 | .999 | E1A100 | |||||
| rs12922317 | 16 | TNFRSF17 | Intron,Tag-SNP | G | 0.29 | 0.3958 | A | .011 | 0.6234 | 0.4317 | 0.9004 | .010 | Myeloma IX | rs11862958 |
| G | 0.2778 | 0.4 | A | .428 | 0.5769 | 0.1473 | 2.26 | .380 | Hovon-50 | rs11862958 | ||||
| G | 0.1667 | 0.36 | A | .198 | 0.3556 | 0.07006 | 1.804 | .800 | E1A100 | rs11862958 | ||||
| rs2440 | 2 | XRCC5 | Untranslated | T | 0.4286 | 0.3486 | C | .062 | 1.401 | 0.9828 | 1.998 | .047 | Myeloma IX | rs207932 |
| T | 0.25 | 0.1818 | C | .611 | 1.5 | 0.3131 | 7.186 | .857 | Hovon-50 | rs207932 | ||||
| T | 0.4167 | 0.2292 | C | .189 | 2.403 | 0.6351 | 9.088 | .226 | E1A100 | rs207932 |
NA indicates not applicable; L95, lower 95% CI; and U95, upper 95% CI.