Table 1.
Top Predicted Genes for Crohn Disease
| Gene | LBF | p Value | GWAS Hit | Supporting Evidence | p Value (Rep.) |
|---|---|---|---|---|---|
| UBE2L3 | 7.78 | 2.2 × 10−6 | no | associated with celiac disease, rheumatoid arthritis, and lupus34 | 4.2 × 10−6 |
| ORMDL3 | 5.72 | 3.3 × 10−5 | yes | associated with Crohn disease and ulcerative colitis29,33 | 1.0 × 10−6 |
| PTGER4 | 5.57 | 3.7 × 10−5 | yes | associated with Crohn disease33 | 3.4 × 10−5 |
| IK | 5.43 | 4.3 × 10−5 | no | regulates class II MHC antigen, which is associated with autoimmune diseases38 | 0.75 |
| LYNX1 | 5.34 | 4.8 × 10−5 | no | agonist of nonneuronal nAchR pathway, which may be important for IBD39–41 | 0.014 |
| NUDT4 | 5.32 | 4.8 × 10−5 | no | NA | 3.4 × 10−5 |
| EFS | 5.23 | 6.1 × 10−5 | no | knockout mice exhibit symptoms similar to Crohn disease36,37 | 0.039 |
| FAM96A | 5.19 | 6.3 × 10−5 | no | NA | 4.2 × 10−6 |
| SLC22A5 | 5.17 | 6.3 × 10−5 | yes | associated with Crohn disease29,33 | 3.8 × 10−5 |
| ANAPC2 | 4.87 | 9.2 × 10−5 | no | NA | 0.0006 |
The LBF column is the logarithm of the Bayes Factor for the genes. The p values refer to the p values of LBFs, calculated from simulations. The “GWAS hit” column shows whether a gene has been implicated as a candidate gene in previous GWASs. The last column shows the p value of the genes using an independent GWAS data set of Crohn disease (replication). See the text for details of the supporting evidence.