TABLE 1.
Summary of the GWA study performed in 946 patients with ileal CD and 977 controls and the replication studies performed in 530 trios with ileal CD (Replication #1) and 350 cases with ileal CD and 207 controls (Replication #2)
| RANK |
#SNPs |
CHR |
RS# |
GWA |
REPLICATION #1 |
REPLICATION #2 |
COMBINED REPLICATION |
GENE |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF iCD |
MAF CTL |
P-VALUE |
T |
U |
MAF iCD |
MAF CTL |
OR |
P-VALUE |
|||||
| 1 | 8 | 16 | rs2076756 | 0.358 | 0.244 | 7.01E-14 | P.T. | P.T. | P.T. | P.T. | P.T. | P.T. | CARD15 |
| 2 | 13 | 1 | rs7517847 | 0.295 | 0.403 | 3.06E-12 | P.T. | P.T. | P.T. | P.T. | P.T. | P.T. | IL23R |
| 3 | 3 | 2 | rs2241880 | 0.364 | 0.453 | 6.38E-08 | 220 | 306 | 0.353 | 0.478 | 0.68 | 4.1 E-08 | ATG16L1 |
| 4 | 1 | 4 | rs16853571 | 0.038 | 0.077 | 7.68E-07 | 39 | 75 | 0.057 | 0.047 | 0.69 | 0.0084 | PHOX2B |
| 5 | 1 | 12 | rs886898 | 0.156 | 0.102 | 1.93E-06 | 121 | 136 | N.D. | N.D. | N.D. | N.D. | - |
| 6 | 2 | 1 | rs2343331 | 0.279 | 0.212 | 2.49E-06 | Failed | Failed | N.D. | N.D. | N.D. | N.D. | - |
| 7 | 1 | 18 | rs937815 | 0.054 | 0.094 | 3.25E-06 | 96 | 99 | N.D. | N.D. | N.D. | N.D. | - |
| 8 | 1 | 3 | rs6439924 | 0.218 | 0.160 | 6.00E-06 | 166 | 140 | N.D. | N.D. | N.D. | N.D. | - |
| 9 | 1 | 10 | rs224136 | 0.134 | 0.191 | 7.90E-06 | 94 | 149 | 0.140 | 0.230 | 0.60 | 2.9 E-07 | intergenic |
| 10 | 1 | 9 | rs10821091 | 0.399 | 0.332 | 1.44E-05 | 274 | 252 | N.D. | N.D. | N.D. | N.D. | - |
| 10 | 1 | 14 | rs1188157 | 0.487 | 0.417 | 1.58E-05 | 254 | 240 | N.D. | N.D. | N.D. | N.D. | - |
| 12 | 1 | 1 | rs2819130 | 0.177 | 0.126 | 2.10E-05 | 130 | 144 | N.D. | N.D. | N.D. | N.D. | - |
| 13 | 1 | 11 | rs2712800 | 0.373 | 0.441 | 2.38E-05 | 242 | 222 | N.D. | N.D. | N.D. | N.D. | - |
| 14 | 1 | 22 | rs4821544 | 0.397 | 0.333 | 2.89E-05 | 267 | 221 | 0.374 | 0.339 | 1.19 | 0.0090 | NCF4 |
| 15 | 1 | 2 | rs6733000 | 0.081 | 0.124 | 3.03E-05 | 81 | 77 | N.D. | N.D. | N.D. | N.D. | - |
| 16 | 1 | 2 | rs7603516 | 0.064 | 0.102 | 3.10E-05 | 73 | 62 | N.D. | N.D. | N.D. | N.D. | - |
| 17 | 1 | 16 | rs8050910 | 0.388 | 0.458 | 3.28E-05 | 221 | 271 | 0.400 | 0.430 | 0.84 | 0.0085 | FAM92B |
| 18 | 2 | 1 | rs2490271 | 0.206 | 0.152 | 3.44E-05 | 175 | 166 | N.D. | N.D. | N.D. | N.D. | - |
| 19 | 1 | 20 | rs4810663 | 0.236 | 0.180 | 3.45E-05 | 182 | 178 | N.D. | N.D. | N.D. | N.D. | - |
| 20 | 1 | 8 | rs10505007 | 0.400 | 0.332 | 3.78E-05 | 221 | 248 | N.D. | N.D. | N.D. | N.D. | - |
| 21 | 1 | 8 | rs2044999 | 0.330 | 0.395 | 3.84E-05 | NT | NT | N.D. | N.D. | N.D. | N.D. | - |
| 22 | 1 | 9 | rs4878061 | 0.418 | 0.485 | 4.64E-05 | NT | NT | N.D. | N.D. | N.D. | N.D. | - |
| 23 | 1 | 13 | rs11617463 | 0.044 | 0.077 | 4.85E-05 | 59 | 80 | Failed | Failed | N.D. | N.D. | - |
#SNPs= number of significant SNPs (Pvalue < 3e-05) in GWA analysis for the given locus; MAF iCD= minor allele frequency in ileal CD patients in GWA study and Replication #2; MAF CTL= minor allele frequency in controls in GWA study and Replication #2; T= number of transmissions of the minor allele in Replication #1; U= number of non transmissions of the minor allele in Replication #1; NT= not tested (e.g. failed to be designed); Failed= failed genotyping; P.T. = previously tested in these samples and having confirmed replication. N.B. P-values for the GWA results are two-tailed and for the combined replication study one-tailed. All 23 loci were included in Replication #1. All six loci that were replicated in Replication #1 - having P-value <0.05 (shown in bold) – were included in Replication #2. Mantel-Haenszel ORs and p-values are reported for the combined replication data only. For additional detail regarding the results from the two replication studies, please see Supplementary Table 1 online.