Statistics
| Case | Control |
|---|---|
| 24435 | 435759 |
Phenotype Definition
The presence of a neoplasm of the small intestine. [HPO:probinson]
Phenotype Comment
An estimated 40% of small bowel cancers are adenocarcinomas, 40% are carcinoids, 15% are sarcomas (GI stromal tumors), and less than 5% are lymphomas.
Top SNP Information
| Location | SNP | Gene | Ref>Alt | Alt in Case | Alt in Control | Chi-square | P-value | Odds ratio |
|---|---|---|---|---|---|---|---|---|
| chr15:48426484 | rs1426654 | SLC24A5 | A>G | 1049 | 26477 | 116.9 | 2.994e-27 | 0.7101 |
| chr15:48392165 | rs1834640 | - | A>G | 1237 | 30387 | 116.8 | 3.129e-27 | 0.729 |
| chr5:33951693 | rs16891982 | SLC45A2 | G>C | 2915 | 64143 | 116.3 | 4.004e-27 | 0.8106 |
| chr1:159174683 | rs2814778 | ACKR1 | T>C | 700 | 18677 | 105.9 | 7.93e-25 | 0.6728 |
| chr5:33958959 | rs28777 | SLC45A2 | A>C | 2468 | 54524 | 101.4 | 7.344e-24 | 0.8089 |
| chr5:147671850 | rs7724380 | - | G>A | 745 | 19438 | 99.74 | 1.734e-23 | 0.6883 |
| chr17:58508582 | rs8071181 | C17orf64 | G>A | 544 | 14873 | 92.75 | 5.936e-22 | 0.6573 |
| chr5:147666044 | rs7707813 | - | T>C | 697 | 18066 | 89.96 | 2.426e-21 | 0.693 |
| chr5:147863034 | rs9325101 | HTR4 | A>G | 612 | 16128 | 86.56 | 1.353e-20 | 0.6817 |
| chr8:145639681 | rs1871534 | SLC39A4 | G>C | 675 | 17470 | 86.35 | 1.51e-20 | 0.6942 |
| chr9:117110112 | Affx-52344420 | AKNA | T>TG | 517 | 14062 | 85.8 | 1.987e-20 | 0.661 |
| chr7:38331504 | rs1860521 | - | C>T | 667 | 17254 | 84.95 | 3.053e-20 | 0.6948 |
| chr14:99587529 | rs10145157 | - | T>C | 615 | 16066 | 82.76 | 9.262e-20 | 0.688 |
| chr17:58786625 | rs2643103 | BCAS3 | G>A | 734 | 18524 | 81.31 | 1.927e-19 | 0.7116 |
| chr5:33951116 | rs35397 | SLC45A2 | T>G | 4167 | 85941 | 76.56 | 2.138e-18 | 0.8652 |
| chr9:140957557 | rs11137360 | CACNA1B | A>G | 822 | 20184 | 76.38 | 2.346e-18 | 0.7318 |
| chr3:391100 | rs13060847 | CHL1 | G>A | 403 | 11251 | 75.67 | 3.348e-18 | 0.6445 |
| chr13:113979968 | rs200506581 | GRTP1 | C>CCACA | 450 | 12276 | 75.54 | 3.581e-18 | 0.6596 |
| chr17:29290106 | rs55861543 | - | C>T | 813 | 19946 | 75.09 | 4.508e-18 | 0.7325 |
| chr2:171380643 | rs34020565 | MYO3B | T>G | 1003 | 23856 | 74.98 | 4.756e-18 | 0.755 |
| chr20:60968596 | rs1570027 | CABLES2 | A>G | 10323 | 197433 | 62.19 | 3.118e-15 | 0.9142 |
| chr20:60920700 | rs6143035 | LAMA5 | T>C | 11311 | 215264 | 60.81 | 6.296e-15 | 0.9177 |
| chr20:60899182 | rs11698080 | LAMA5 | C>T | 10070 | 192030 | 56.9 | 4.594e-14 | 0.9167 |
| chr20:60898244 | rs57627107 | LAMA5 | A>G | 10507 | 200128 | 55.68 | 8.509e-14 | 0.919 |
| chr8:117630683 | rs16892766 | - | A>C | 4310 | 68802 | 54.11 | 1.898e-13 | 1.128 |
| chr18:46453463 | rs4939827 | SMAD7 | T>C | 22520 | 416158 | 51.44 | 7.365e-13 | 0.9352 |
| chr20:60921044 | rs4925386 | LAMA5 | C>T | 14730 | 275339 | 46.22 | 1.058e-11 | 0.9335 |
| chr6:55708497 | rs2023523 | BMP5 | A>G | 18895 | 350118 | 45.39 | 1.611e-11 | 0.9377 |
| chr8:117640315 | rs11986063 | - | C>T | 4641 | 75745 | 37.98 | 7.15e-10 | 1.103 |
| chr18:46453754 | rs35352860 | SMAD7 | C>T | 12471 | 233052 | 35.83 | 2.157e-09 | 0.9382 |
| chr20:6326507 | rs6085506 | - | C>T | 19385 | 334014 | 35.71 | 2.293e-09 | 1.059 |
| chr15:32994756 | rs4779584 | - | C>T | 9749 | 164426 | 35.55 | 2.49e-09 | 1.072 |
| chr6:55715715 | rs12215796 | BMP5 | G>A | 21948 | 403404 | 34.99 | 3.322e-09 | 0.9462 |
| chr20:60894470 | rs2297588 | LAMA5 | C>T | 14893 | 276567 | 34.28 | 4.771e-09 | 0.9426 |
| chr15:33022090 | rs35330276 | GREM1 | G>A | 9574 | 161648 | 33.6 | 6.756e-09 | 1.07 |
| chr2:213171295 | rs982765 | ERBB4 | G>T | 5145 | 84936 | 33.0 | 9.197e-09 | 1.091 |
| chr15:32992658 | rs28399071 | - | G>A | 4932 | 81159 | 32.98 | 9.311e-09 | 1.093 |
| chr7:46919215 | rs6463354 | - | G>A | 19590 | 338012 | 32.74 | 1.056e-08 | 1.056 |
| chr20:6404281 | rs961253 | - | C>A | 18023 | 310524 | 32.2 | 1.393e-08 | 1.056 |
| chr5:134458908 | rs646506 | - | A>G | 22866 | 419330 | 31.83 | 1.679e-08 | 0.9487 |
| Location | SNP | Gene | Ref>Alt | Alt in Case | Alt in Control | Chi-square | P-value | Odds ratio |
|---|---|---|---|---|---|---|---|---|
| chr14:99587529 | rs10145157 | - | T>C | 615 | 2210 | 35.62 | 2.402e-09 | 0.7611 |
| chr8:117630683 | rs16892766 | - | A>C | 4550 | 11306 | 35.29 | 2.838e-09 | 1.115 |
| chr20:60968596 | rs1570027 | CABLES2 | A>G | 10815 | 31407 | 32.3 | 1.318e-08 | 0.931 |
| chr20:60921044 | rs4925386 | LAMA5 | C>T | 15820 | 45268 | 30.1 | 4.103e-08 | 0.9407 |
| chr20:60920700 | rs6143035 | LAMA5 | T>C | 11864 | 34247 | 29.58 | 5.364e-08 | 0.9359 |
| chr23:51242000 | rs149912987 | - | G>A | 1820 | 4424 | 28.22 | 1.081e-07 | 1.163 |
| chr6:55708497 | rs2023523 | BMP5 | A>G | 19843 | 56304 | 27.92 | 1.262e-07 | 0.9456 |
| chr20:60898244 | rs57627107 | LAMA5 | A>G | 11013 | 31808 | 26.55 | 2.572e-07 | 0.9375 |
| chr9:136137065 | rs687621 | ABO | A>G | 16013 | 45666 | 25.3 | 4.906e-07 | 0.9456 |
| chr9:136142203 | rs514659 | ABO | A>C | 15451 | 44070 | 24.72 | 6.626e-07 | 0.9455 |
| chr9:136143442 | rs612169 | ABO | A>G | 16063 | 45774 | 24.5 | 7.432e-07 | 0.9466 |
| chr20:60899182 | rs11698080 | LAMA5 | C>T | 10569 | 30477 | 23.8 | 1.071e-06 | 0.9397 |
| chr5:9923143 | rs73742912 | - | A>G | 9955 | 25962 | 23.75 | 1.099e-06 | 1.066 |
| chr18:46453463 | rs4939827 | SMAD7 | T>C | 24031 | 67745 | 23.74 | 1.102e-06 | 0.9508 |
| chr4:60360891 | rs116040389 | - | C>T | 513 | 1791 | 23.37 | 1.333e-06 | 0.7844 |
| chr2:72356303 | rs7583202 | - | A>G | 977 | 3193 | 23.17 | 1.484e-06 | 0.8373 |
| chr9:136149229 | rs505922 | ABO | T>C | 15901 | 45308 | 23.06 | 1.57e-06 | 0.948 |
| chr4:27334027 | rs75790656 | - | G>T | 1734 | 4166 | 22.56 | 2.041e-06 | 1.148 |
| chr4:121412352 | rs115369301 | - | C>T | 816 | 1834 | 22.54 | 2.058e-06 | 1.223 |
| chr8:117640315 | rs11986063 | - | C>T | 4986 | 12706 | 22.19 | 2.473e-06 | 1.086 |
| chr8:117630683 | rs16892766 | - | A>C | 4310 | 10600 | 36.92 | 1.228e-09 | 1.122 |
| chr20:60968596 | rs1570027 | CABLES2 | A>G | 10323 | 29872 | 32.29 | 1.327e-08 | 0.9294 |
| chr20:60920700 | rs6143035 | LAMA5 | T>C | 11311 | 32505 | 28.72 | 8.375e-08 | 0.9353 |
| chr20:60898244 | rs57627107 | LAMA5 | A>G | 10507 | 30302 | 28.72 | 8.372e-08 | 0.9336 |
| chr2:213171295 | rs982765 | ERBB4 | G>T | 5145 | 12974 | 27.78 | 1.361e-07 | 1.096 |
| chr6:55708497 | rs2023523 | BMP5 | A>G | 18895 | 53363 | 27.13 | 1.905e-07 | 0.9451 |
| chr20:60899182 | rs11698080 | LAMA5 | C>T | 10070 | 29017 | 26.92 | 2.12e-07 | 0.9344 |
| chr4:28263120 | rs7690507 | - | T>G | 7148 | 18309 | 25.25 | 5.036e-07 | 1.079 |
| chr23:51242000 | rs149912987 | - | G>A | 1801 | 4385 | 25.15 | 5.315e-07 | 1.155 |
| chr4:60360891 | rs116040389 | - | C>T | 490 | 1722 | 24.6 | 7.048e-07 | 0.7752 |
| chr4:28246487 | rs11734756 | - | G>A | 5893 | 15030 | 23.89 | 1.019e-06 | 1.083 |
| chr8:117640315 | rs11986063 | - | C>T | 4641 | 11705 | 23.68 | 1.138e-06 | 1.093 |
| chr20:60855449 | rs28653375 | OSBPL2 | C>T | 9645 | 27717 | 23.47 | 1.266e-06 | 0.9379 |
| chr14:93078988 | rs9788457 | RIN3 | T>C | 5340 | 15671 | 23.14 | 1.503e-06 | 0.9223 |
| chr2:213168768 | rs7588550 | ERBB4 | A>G | 2184 | 5301 | 22.61 | 1.983e-06 | 1.132 |
| chr4:121412352 | rs115369301 | - | C>T | 810 | 1809 | 22.58 | 2.014e-06 | 1.224 |
| chr20:60921044 | rs4925386 | LAMA5 | C>T | 14730 | 41757 | 22.1 | 2.583e-06 | 0.9474 |
| chr11:110023537 | rs17714368 | RDX | C>T | 1893 | 5840 | 22.04 | 2.676e-06 | 0.8811 |
| chr5:9923143 | rs73742912 | - | A>G | 9549 | 24803 | 21.87 | 2.924e-06 | 1.065 |
| chr6:55708204 | rs17678251 | BMP5 | C>A | 12082 | 34453 | 21.75 | 3.098e-06 | 0.9446 |
Associated Diseases ⓘ
| ID | Name | Top Correlation |
|---|---|---|
| ICD: K317 | Polyp of stomach and duodenum | 6/20 |
| ICD: K635 | Polyp of colon | 9/20 |