Table 3. List of the 73 variants selected for validation.
Abbreviations: Chr, Chromosome; Ref, reference allele; Obs, observed allele; HOM, homozygous; HET, heterozygous; Func, variant function; SNPs, single nucleotide variants/polymorphisms; MAF, minor allele frequency; GoNL, Genome of the Netherlands project database, 498 unrelated Dutch individuals; EVS_EA, NHLBI Exome Sequencing Project database, 4,300 European-American unrelated individuals; 1000G, 1000 Genomes Project, 2,500 individuals from about 25 populations around the world; GIFT, Genetics In Familial Thrombosis study, 96 unrelated VTE cases with positive family history of VTE; GoNL, Genome of the Netherlands project database, 498 unrelated Dutch individuals.
| Chr | Start | End | Ref | Obs | Func | Gene | Exonic Func | dbSNP135 | MAF EA_6500_% | MAF GIFT_% (assuming_allCalled) | MAF 1000G 2012apr_ALL_% | GoNL number of genotypes (HOM_Ref/HET/HOM_Obs) | Filter strategy |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1905479 | 1905479 | C | T | exonic | KIAA1751 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 1 | 6211042 | 6211042 | C | G | intronic | CHD5 | 0.05 | 0.00 | 0 | NA | 2 | ||
| 1 | 27688743 | 27688743 | T | C | splicing | MAP3K6 | rs55841735 | 0.41 | 1.56 | 0.41 | 494/4/0 | 2.3 | |
| 1 | 117122285 | 117122285 | - | TCC | exonic | IGSF3 | nonframeshift insertion | NA | 21.77 | 0 | NA | 2 | |
| 1 | 156354348 | 156354348 | C | - | splicing | RHBG | rs11303415 | NA | 0.00 | 0 | NA | 2 | |
| 1 | 231377078 | 231377078 | C | A | UTR5 | GNPAT | 0.01 | 0.00 | 0 | 493/1/0 | 2 | ||
| 1 | 234536943 | 234536943 | T | G | exonic | TARBP1 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 2 | 43965641 | 43965641 | T | C | exonic | PLEKHH2 | synonymous SNP | NA | 0.52 | 0 | NA | 2 | |
| 2 | 44184604 | 44184604 | T | C | intronic | LRPPRC | 0.02 | 0.52 | 0 | NA | 2.3 | ||
| 2 | 45640302 | 45640302 | G | C | exonic | SRBD1 | nonsynonymous SNP | rs34959371 | 0.43 | 1.04 | 0.27 | 497/1/0 | 2.3 |
| 2 | 207175476 | 207175476 | G | T | exonic | ZDBF2 | nonsynonymous SNP | rs36095066 | 0.87 | 0.00 | 0.46 | 493/5/0 | 2 |
| 3 | 42251580 | 42251580 | - | GGA | exonic | TRAK1 | nonframeshift insertion | NA | 0.00 | 0 | NA | 2 | |
| 3 | 107932728 | 107932728 | G | A | intronic | IFT57 | 0.40 | 0.52 | 0.09 | 496/2/0 | 2 | ||
| 3 | 111667982 | 111667982 | C | T | intronic | PHLDB2 | rs116705395 | NA | 0.00 | 0.18 | 497/1/0 | 2 | |
| 3 | 121097497 | 121097497 | C | T | intronic | STXBP5L | rs182808568 | NA | 0.00 | 0.14 | 494/4/0 | 2 | |
| 3 | 121260373 | 121260373 | G | A | intronic | POLQ | rs183249693 | 0.08 | 0.00 | 0.09 | 494/4/0 | 2 | |
| 3 | 124829057 | 124829057 | A | G | exonic | SLC12A8 | synonymous SNP | rs11714448 | 3.09 | 6.25 | 1 | 470/28/0 | 3 |
| 3 | 129308276 | 129308276 | G | A | exonic | PLXND1 | nonsynonymous SNP | rs146072632 | 0.21 | 0.00 | 0 | 481/1/0 | 2 |
| 3 | 195510838 | 195510838 | G | A | exonic | MUC4 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 3 | 195591020 | 195591020 | T | G | UTR3 | TNK2 | rs112362099 | 1.00 | 2.60 | 1 | 480/18/0 | 3 | |
| 4 | 144346515 | 144346515 | C | G | intronic | GAB1 | rs187533266 | NA | 0.00 | 0.23 | 497/1/0 | 2 | |
| 5 | 176305151 | 176305151 | C | A | intronic | UNC5A | 0.01 | 0.00 | 0 | NA | 2 | ||
| 5 | 180661310 | 180661310 | G | T | exonic | TRIM41 | synonymous SNP | 0.03 | 0.00 | 0 | NA | 2 | |
| 7 | 100016781 | 100016781 | T | C | exonic | ZCWPW1 | nonsynonymous SNP | rs141450215 | 0.50 | 0.00 | 0.27 | 496/2/0 | 2 |
| 7 | 103061356 | 103061356 | T | A | intronic | SLC26A5 | NA | 0.00 | 0 | 497/1/0 | 2 | ||
| 7 | 110763503 | 110763503 | A | G | exonic | LRRN3 | synonymous SNP | rs35229264 | 0.47 | 0.00 | 0.09 | 495/3/0 | 2 |
| 7 | 111936315 | 111936315 | C | T | exonic | ZNF277 | synonymous SNP | rs142208106 | 0.00 | 0.00 | 0 | 496/2/0 | 2 |
| 7 | 127229265 | 127229265 | C | T | intronic | ARF5 | 0.56 | 1.56 | 0.23 | 487/4/0 | 2 | ||
| 7 | 127239585 | 127239585 | C | T | exonic | FSCN3 | nonsynonymous SNP | rs34941808 | 0.60 | 1.56 | 0.14 | 495/3/0 | 2.3 |
| 9 | 2039776 | 2039776 | - | CAG | exonic | SMARCA2 | nonframeshift insertion | NA | 11.54 | 0 | NA | 2 | |
| 9 | 2648286 | 2648286 | G | A | exonic | VLDLR | nonsynonymous SNP | rs35339834 | 0.13 | 0.00 | 0.05 | 497/1/0 | 2 |
| 9 | 5919929 | 5919929 | T | C | exonic | KIAA2026 | nonsynonymous SNP | 0.07 | 0.00 | 0 | NA | 2 | |
| 9 | 8486132 | 8486132 | G | C | exonic | PTPRD | synonymous SNP | rs144111555 | 0.10 | 0.00 | 0.27 | 496/2/0 | 2 |
| 9 | 136917482 | 136917482 | G | A | exonic | BRD3 | synonymous SNP | rs61731642 | 0.00 | 0.00 | 0.09 | NA | 2 |
| 9 | 140145895 | 140145895 | C | G | ncRNA_intronic | LOC100129722 | 0.17 | 0.52 | 0 | NA | 2 | ||
| 10 | 21318672 | 21318672 | A | C | intronic | NEBL | rs61849814 | NA | 1.04 | 0 | NA | 2 | |
| 11 | 62601915 | 62601915 | G | A | exonic | WDR74 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 11 | 63883847 | 63883847 | C | T | exonic | FLRT1 | synonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 11 | 65293664 | 65293664 | G | A | exonic | SCYL1 | nonsynonymous SNP | 0.01 | 0.00 | 0 | NA | 2 | |
| 11 | 66472221 | 66472221 | G | A | exonic | SPTBN2 | synonymous SNP | rs144939155 | 0.25 | 0.52 | 0.18 | 479/3/0 | 2 |
| 11 | 66638474 | 66638474 | C | A | intronic | PC | NA | 0.00 | 0 | NA | 2 | ||
| 11 | 68177405 | 68177405 | C | T | exonic | LRP5 | synonymous SNP | rs145456776 | 0.03 | 0.00 | 0 | NA | 2 |
| 12 | 130919182 | 130919182 | G | A | intronic | RIMBP2 | NA | 0.00 | 0 | NA | 2 | ||
| 12 | 131311749 | 131311749 | A | C | exonic | STX2 | nonsynonymous SNP | rs137928907 | 2.55 | 2.08 | 1 | 463/32/1 | 1 |
| 12 | 133306808 | 133306808 | C | T | exonic | ANKLE2 | nonsynonymous SNP | rs149597645 | 1.63 | 3.65 | 1 | 477/21/0 | 3 |
| 13 | 113824899 | 113824899 | T | C | intronic | PROZ | rs3024787 | NA | 0.00 | 0 | 493/5/0 | 2 | |
| 14 | 105360291 | 105360291 | C | G | intronic | KIAA0284 | rs185909273 | NA | 0.00 | 0.18 | 496/2/0 | 2 | |
| 14 | 105418571 | 105418571 | C | T | exonic | AHNAK2 | nonsynonymous SNP | 0.00 | 0.00 | 0 | NA | 2 | |
| 16 | 602505 | 602505 | C | T | exonic | SOLH | synonymous SNP | 0.00 | 0.00 | 0 | NA | 2 | |
| 16 | 4940366 | 4940366 | A | G | intronic | PPL | 0.14 | 0.52 | 0.18 | 497/1/0 | 2 | ||
| 16 | 5083391 | 5083391 | C | G | exonic | NAGPA | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 17 | 45360730 | 45360730 | T | C | exonic | ITGB3 | nonsynonymous SNP | rs5918 | 15.17 | 14.58 | 9 | 341/145/12 | 1 |
| 17 | 64210757 | 64210757 | C | A | exonic | APOH | nonsynonymous SNP | rs4581 | 23.76 | 21.88 | 47 | 311/166/21 | 1 |
| 17 | 65713943 | 65713943 | - | A | upstream | NOL11 | NA | 0.00 | 0 | NA | 2 | ||
| 17 | 66274384 | 66274384 | C | T | exonic | SLC16A6 | synonymous SNP | rs149995088 | 0.29 | 0.52 | 0.09 | 494/4/0 | 2 |
| 17 | 67310584 | 67310584 | A | G | UTR5 | ABCA5 | NA | 0.00 | 0 | NA | 2 | ||
| 17 | 72443156 | 72443156 | G | A | exonic | GPRC5C | nonsynonymous SNP | rs142232982 | 0.05 | 0.00 | 0.09 | NA | 2 |
| 17 | 72740355 | 72740355 | G | A | intronic | RAB37 | NA | 0.00 | 0 | NA | 2 | ||
| 18 | 43496563 | 43496563 | G | A | intronic | EPG5 | 0.12 | 0.00 | 0 | 497/1/0 | 2 | ||
| 19 | 15569378 | 15569378 | G | C | exonic | RASAL3 | nonsynonymous SNP | rs58123634 | 4.84 | 6.77 | 3 | 457/25/0 | 3 |
| 19 | 47207685 | 47207685 | G | C | intronic | PRKD2 | 0.08 | 0.00 | 0 | 494/1/0 | 2 | ||
| 19 | 49254538 | 49254538 | T | G | exonic | FUT1 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 19 | 49713534 | 49713534 | G | A | exonic | TRPM4 | nonsynonymous SNP | NA | 0.00 | 0 | NA | 2 | |
| 19 | 49878275 | 49878275 | G | A | exonic | DKKL1 | nonsynonymous SNP | rs35389403 | 0.33 | 0.00 | 1 | NA | 2 |
| 19 | 49910139 | 49910139 | C | G | intronic | CCDC155 | rs112074780 | 0.39 | 0.00 | 1 | NA | 2 | |
| 19 | 50163098 | 50163098 | G | A | intronic | IRF3 | NA | 0.00 | 0 | NA | 2 | ||
| 19 | 51503285 | 51503285 | C | T | exonic | KLK8 | nonsynonymous SNP | rs16988799 | 5.15 | 2.60 | 5 | 441/56/1 | 1 |
| 19 | 51528041 | 51528041 | C | T | exonic | KLK11 | nonsynonymous SNP | rs3745539 | 7.53 | 7.29 | 6 | 421/71/5 | 1 |
| 19 | 53454862 | 53454862 | T | C | intronic | ZNF816 | 0.08 | 0.52 | 0 | 497/1/0 | 2.3 | ||
| 20 | 744270 | 744270 | G | A | exonic | SLC52A3 | synonymous SNP | rs139430185 | 0.05 | 0.00 | 0 | 497/1/0 | 2 |
| 22 | 38890624 | 38890624 | A | C | intronic | DDX17 | NA | 0.00 | 0 | 497/1/0 | 2 | ||
| 22 | 41736075 | 41736075 | C | A | exonic | ZC3H7B | synonymous SNP | NA | 0.00 | 0 | 494/2/0 | 2 | |
| X | 117702143 | 117702143 | C | G | intronic | DOCK11 | 0.07 | 0 | NA | 2 |