Table 2.
Evidence of Multiple Independent Effects in Disease-Associated Loci under Penalized and Conditional Regression Analyses
| Chr | Locus | Reported Associations (p Value in Current Samples) | Independent SNPs (and p Values Conditioned on All Other SNPs) | Genomic Context of Independent SNPs |
|---|---|---|---|---|
| CD | ||||
| 6 | CDKAL1(MIM 611259) | rs6908425 (intron 3) | rs6908425 (2.9 × 10−5), rs898165 (4.6 × 10−7) | rs6908425 (intron 3), rs898165 (intron 13) |
| 12 | LRRK2 (MIM 609007)–MUC19 (MIM 612170) | rs11175593 (intergenic) | rs7962370 (9.2 × 10−7), rs11175593 (0.0025) | rs7962370 (intergenic), rs11175593 (intergenic) |
| T1D | ||||
| 2 | AFF3 (MIM 601464) | rs9653442 (intergenic) | rs11685258 (3.0 × 10−5), rs2309837 (2.1 × 10−5) | rs11685258 (intron 1), rs2309837 (intergenic) |
| 4 | IL2 (MIM 147680) | rs4505848 (intron 18 of KIAA1109 [MIM 611565]) | rs4505848 (0.0059), rs13152362 (0.00029) | rs4505848, rs13152362 (intron 59 of KIAA1109) |
| T2D | ||||
| 3 | PPARG (MIM 601487)-SYN2 (MIM 600755) | rs13081389a (intergenic) and rs17036101 (intergenic) | rs6775191 (5.3 × 10−6), rs17036101 (0.017) | rs6775191 (intergenic), rs17036101 (intergenic) |
Only common SNPs with additive p ≤ 2.3 × 10−6 in the WTCCC data and those SNPs whose associations were confirmed in the literature were analyzed. The following abbreviations are used: chr, chromosome; CD, Crohn disease; T1D, type 1 diabetes; and T2D, type 2 diabetes.
a
rs13081389 is in perfect LD (r2 = 1) with rs17036101.