Statistics
| Case | Control |
|---|---|
| 9175 | 451019 |
Phenotype Definition
Abnormality of the urachus. [HPO:probinson]
Phenotype Comment
The urachus is a vestigial embryonic structure, a canal that connects the urinary bladder of the fetus with the allantois (a structure involved in the development of the umbilical cord). During embryonic development, the lumen of the urachus is normally obliterated, transforming the urachus into a solid cord.
Top SNP Information
| Location | SNP | Gene | Ref>Alt | Alt in Case | Alt in Control | Chi-square | P-value | Odds ratio |
|---|---|---|---|---|---|---|---|---|
| chr11:111171709 | rs3802842 | COLCA2 | A>C | 6378 | 287319 | 106.0 | 7.427e-25 | 1.173 |
| chr11:111165009 | rs7103178 | - | T>C | 6385 | 288498 | 99.57 | 1.894e-23 | 1.167 |
| chr11:111125512 | rs2001754 | C11orf53 | A>G | 6884 | 315764 | 85.96 | 1.833e-20 | 1.152 |
| chr18:46453463 | rs4939827 | SMAD7 | T>C | 8664 | 467439 | 84.24 | 4.385e-20 | 0.8737 |
| chr15:48426484 | rs1426654 | SLC24A5 | A>G | 331 | 27195 | 83.12 | 7.715e-20 | 0.6045 |
| chr5:33951693 | rs16891982 | SLC45A2 | G>C | 1004 | 66054 | 77.76 | 1.162e-18 | 0.7504 |
| chr15:48392165 | rs1834640 | - | A>G | 404 | 31220 | 77.56 | 1.286e-18 | 0.6426 |
| chr5:33958959 | rs28777 | SLC45A2 | A>C | 835 | 56157 | 74.92 | 4.892e-18 | 0.7353 |
| chr1:159174683 | rs2814778 | ACKR1 | T>C | 224 | 19153 | 65.32 | 6.372e-16 | 0.5828 |
| chr2:163216109 | rs3213843 | GCA | C>T | 123 | 12029 | 57.02 | 4.304e-14 | 0.5098 |
| chr16:28995057 | rs11859822 | SPNS1 | T>C | 398 | 29038 | 56.89 | 4.618e-14 | 0.6822 |
| chr1:64273591 | rs659592 | ROR1 | A>G | 458 | 32459 | 55.75 | 8.23e-14 | 0.702 |
| chr15:45491394 | rs1648299 | SHF | T>C | 201 | 16958 | 55.55 | 9.121e-14 | 0.5912 |
| chr16:28954860 | rs7203982 | - | T>C | 400 | 28982 | 55.34 | 1.014e-13 | 0.6864 |
| chr11:111213944 | rs12365324 | - | G>A | 7978 | 375623 | 54.77 | 1.357e-13 | 1.116 |
| chr8:145639681 | rs1871534 | SLC39A4 | G>C | 218 | 17927 | 54.59 | 1.484e-13 | 0.6058 |
| chr2:171380643 | rs34020565 | MYO3B | T>G | 326 | 24533 | 54.38 | 1.649e-13 | 0.6624 |
| chr16:29035406 | rs74014848 | - | A>G | 274 | 21207 | 52.54 | 4.224e-13 | 0.6438 |
| chr15:89154966 | rs7170666 | - | G>A | 771 | 49975 | 52.34 | 4.674e-13 | 0.7655 |
| chr3:30822859 | rs13316876 | GADL1 | T>C | 644 | 42682 | 51.3 | 7.937e-13 | 0.7495 |
| chr11:111171709 | rs3802842 | COLCA2 | A>C | 6136 | 272007 | 91.79 | 9.629e-22 | 1.163 |
| chr11:111165009 | rs7103178 | - | T>C | 6137 | 272656 | 86.85 | 1.172e-20 | 1.159 |
| chr18:46453463 | rs4939827 | SMAD7 | T>C | 8204 | 430474 | 65.43 | 6.017e-16 | 0.8856 |
| chr11:111125512 | rs2001754 | C11orf53 | A>G | 6706 | 304474 | 64.8 | 8.286e-16 | 1.133 |
| chr8:117630683 | rs16892766 | - | A>C | 1715 | 71397 | 50.24 | 1.36e-12 | 1.199 |
| chr8:117640315 | rs11986063 | - | C>T | 1868 | 78518 | 49.44 | 2.045e-12 | 1.189 |
| chr8:128413305 | rs6983267 | POU5F1B | G>T | 8380 | 434381 | 44.81 | 2.175e-11 | 0.9047 |
| chr12:51213765 | rs11169571 | ATF1 | T>C | 7823 | 362957 | 43.28 | 4.742e-11 | 1.104 |
| chr10:8701219 | rs10795668 | - | G>A | 5554 | 293920 | 43.18 | 5.005e-11 | 0.8989 |
| chr12:51171090 | rs12372718 | ATF1 | A>G | 7829 | 363311 | 41.62 | 1.106e-10 | 1.102 |
| chr8:128407443 | rs10505477 | POU5F1B | A>G | 8561 | 442471 | 41.45 | 1.207e-10 | 0.9082 |
| chr12:51203371 | rs1129406 | ATF1 | C>T | 7832 | 363746 | 41.31 | 1.3e-10 | 1.102 |
| chr11:111213944 | rs12365324 | - | G>A | 7831 | 365648 | 34.62 | 4.01e-09 | 1.093 |
| chr12:51032415 | rs12818741 | DIP2B | A>G | 6859 | 318256 | 34.42 | 4.431e-09 | 1.095 |
| chr18:46453754 | rs35352860 | SMAD7 | C>T | 4559 | 240964 | 32.46 | 1.217e-08 | 0.9064 |
| chr12:50934931 | rs11169484 | DIP2B | G>A | 6811 | 317359 | 31.14 | 2.402e-08 | 1.09 |
| chr17:812750 | rs2955621 | NXN | G>A | 3499 | 156993 | 30.62 | 3.145e-08 | 1.112 |
| chr7:46866208 | rs9791388 | - | C>T | 5658 | 261310 | 30.46 | 3.401e-08 | 1.093 |
| chr18:46459032 | rs4464148 | SMAD7 | T>C | 5852 | 270927 | 29.61 | 5.284e-08 | 1.091 |
| chr12:50901882 | rs10876041 | DIP2B | C>T | 6172 | 320791 | 29.07 | 6.99e-08 | 0.9183 |
| Location | SNP | Gene | Ref>Alt | Alt in Case | Alt in Control | Chi-square | P-value | Odds ratio |
|---|---|---|---|---|---|---|---|---|
| chr11:111171709 | rs3802842 | COLCA2 | A>C | 6136 | 29967 | 67.0 | 2.713e-16 | 1.15 |
| chr11:111165009 | rs7103178 | - | T>C | 6137 | 30085 | 61.62 | 4.169e-15 | 1.144 |
| chr18:46453463 | rs4939827 | SMAD7 | T>C | 8204 | 46901 | 50.59 | 1.135e-12 | 0.8913 |
| chr11:111125512 | rs2001754 | C11orf53 | A>G | 6706 | 33519 | 46.1 | 1.122e-11 | 1.121 |
| chr8:117630683 | rs16892766 | - | A>C | 1715 | 7839 | 40.07 | 2.446e-10 | 1.193 |
| chr8:117640315 | rs11986063 | - | C>T | 1868 | 8642 | 38.21 | 6.363e-10 | 1.181 |
| chr11:111213944 | rs12365324 | - | G>A | 7831 | 39750 | 36.37 | 1.635e-09 | 1.103 |
| chr4:151207127 | rs3749574 | LRBA | C>T | 5591 | 32287 | 35.78 | 2.208e-09 | 0.9011 |
| chr5:40265904 | rs1348612 | - | A>G | 5598 | 27942 | 34.69 | 3.867e-09 | 1.109 |
| chr4:151206319 | rs6817154 | LRBA | T>C | 5600 | 32281 | 34.6 | 4.042e-09 | 0.9026 |
| chr2:44066247 | Affx-20090007 | ABCG8 | G>C | 1221 | 7793 | 34.33 | 4.657e-09 | 0.8298 |
| chr10:8701219 | rs10795668 | - | G>A | 5554 | 31982 | 32.7 | 1.076e-08 | 0.905 |
| chr4:151148930 | rs28405622 | DCLK2 | C>T | 5372 | 30941 | 32.58 | 1.145e-08 | 0.9043 |
| chr4:151199080 | rs2290846 | LRBA | G>A | 5091 | 29394 | 32.37 | 1.277e-08 | 0.9032 |
| chr8:128413305 | rs6983267 | POU5F1B | G>T | 8380 | 47226 | 31.03 | 2.546e-08 | 0.9141 |
| chr2:44065090 | Affx-20089987 | ABCG5 | G>A | 1167 | 7419 | 30.83 | 2.811e-08 | 0.8347 |
| chr12:51213765 | rs11169571 | ATF1 | T>C | 7823 | 39880 | 30.58 | 3.196e-08 | 1.094 |
| chr12:51171090 | rs12372718 | ATF1 | A>G | 7829 | 39910 | 29.9 | 4.553e-08 | 1.093 |
| chr8:128407443 | rs10505477 | POU5F1B | A>G | 8561 | 48123 | 29.31 | 6.183e-08 | 0.9164 |
| chr25:2661556 | rs73188900 | - | A>C | 423 | 1703 | 28.89 | 7.672e-08 | 1.342 |
Associated Diseases ⓘ
| ID | Name | Top Correlation |
|---|---|---|
| ICD: C187 | Sigmoid colon | 2/20 |
| ICD: D125 | Sigmoid colon | 17/20 |
| ID | Name | Top Correlation |
|---|---|---|
| ICD-10: C671 | Dome of bladder | 0/20 |
| ICD-10: K650 | Acute peritonitis | 0/20 |