Table 1. Association results for Crohn's disease prognosis loci.
| Chr | Position (Mb) |
SNP | Risk allele | RAF (ind.) |
OR | 95% CI |
P cohort 1 |
P cohort 2 |
P combined |
Candidate gene or region |
|---|---|---|---|---|---|---|---|---|---|---|
| X | 112.9 | rs5929166 | A | 0.03 | 0.33 | 0.23-0.48 | 1.12 x 10-5 | 5.01 x 10-5 | 4.56 x 10-9 | XACT |
| 6 | 31.7 | rs9279411 | -a | 0.15 | 0.60 | 0.50-0.71 | 1.35 x 10-5 | 7.22 x 10-5 | 5.46 x 10-9 | MHC |
| 6 | 109.0 | rs147856773 | GTGb | 0.12 | 0.57 | 0.47-0.70 | 7.76 x 10-4 | 4.29 x 10-6 | 1.31 x 10-8 | FOXO3 |
| 7 | 45.9 | rs75764599 | A | 0.01 | 3.02 | 2.04-4.49 | 1.73 x 10-3c | 6.25 x 10-6 | 4.32 x 10-8 | IGFBP1/IGFBP3 |
Crohn's disease prognosis SNPs that met genome-wide significance (P <5 × 10-8) in the combined analysis and nominal significance (P <0.05) in both individual cohorts.
The odds ratio is presented with respect to the minor allele and the risk of poor prognosis CD. Allele frequency data is presented for the good prognosis CD cohort.
a
AG deletion
b
Insertion
c
rs75764599 could not be imputed in cohort 1 because of low linkage disequilibrium at this locus, and was therefore directly genotyped using a TaqMan SNP genotyping assay.
Chr, Chromosome; RAF, Risk Allele Frequency; ind., Indolent (good prognosis) CD; OR, odds ratio; 95% CI, 95% confidence interval for OR.