Table 3.
Variance in Liability Explained by the Independent Effects as Identified in the Conditional Logistic Regression Analysis
| Chr | Locus | Independent SNPs and Disease Variance Explained (in Liability Scale)1 | Reported SNPs and Disease Variance Explained | |
|---|---|---|---|---|
| CD (Prevalence = 0.1%) | ||||
| 1 | IL23R (MIM 607562) | rs11465804 (0.87%) rs7517847 (0.47%) | total: 1.34% | rs11465804 (1.12%) |
| 5 | PTGER4 (MIM 601586) | rs4613763 (0.10%), rs6888952 (0.37%), rs9283753 (0.09%) | total: 0.56% | rs4613763 (0.35%) |
| 6 | CDKAL1 (MIM 611259) | rs6908425 (0.13%), rs898165 (0.16%) | total: 0.28% | rs6908425 (0.14%) |
| 12 | LRRK2 (MIM 609007)-MUC19)MIM 612170) | rs11175593 (0.04%), rs7962370 (0.14%) | total: 0.18% | rs11175593 (0.06%) |
| 16 | NOD2 (MIM 605956) | rs2076756 (0.33%), rs8056611 (0.11%) | total: 0.44% | rs2067085 (0.25%) |
| total: 2.66% | total: 1.92% | |||
| T1D (Prevalence = 0.5%) | ||||
| 2 | AFF3 (MIM 601464) | rs11685258 (0.19%), rs2309837 (0.15%) | total: 0.34% | rs9653442 (0.15%) |
| 4 | IL2 (MIM 147680) | rs4505848 (0.07%) rs13152362 (0.14%) | total: 0.21% | rs4505848 (0.16%) |
| 10 | IL2RA (MIM 147730) | rs12722495 (0.32%), rs7096384 (0.14%) | total: 0.46% | rs12251307 (0.20%) |
| 16 | CLEC16A (MIM 611303) | rs7205474 (0.25%), rs2867880 (0.26%) | total: 0.51% | rs12708716 (0.28%) |
| total: 1.48% | total: 0.77% | |||
| T2D (Prevalence = 5.0%) | ||||
| 3 | PPARG (MIM 601487)-SYN2 (MIM 600755) | rs17036101 (0.12%), rs6775191 (0.36%) | total: 0.48% | rs17036101 (0.20%) |
| 12 | TSPAN8 (MIM 600769)-LGR5 (MIM 606667) | rs1705232 (0.98%), rs6581998 (0.14%) | total: 1.12% | rs4760790 (0.47%) |
| total: 1.54% | total: 0.67% | |||
The following abbreviations are used: chr, chromosome; CD, Crohn disease; T1D, type 1 diabetes; and T2D, type 2 diabetes.
1
Adjusted ORs were obtained with multiple logistic regressions for individual independent SNPs either within or across loci. Genotype relative risks were estimated according to a multiplicative model, and explained variance was estimated with the R software reported by So et al.34 Total explained variance was the sum of such estimates from each of the individual SNPs either within or across loci.