Table 5.
Some significant risk loci identified by HWE or LRT-H, but not by the other two tests. Each risk locus is within 250 Kb of some previously identified SNPs or loci. For each risk locus, the LD-independent SNP along with the MAF in the control group and the p-values of LRT-H (PLRT-H) and the HWE exact test (PHWE) are reported.
| Disease | CHR | SNP | BP (in Mb) | MAFcontrol | PLRT-H | PHWE | Reported genes | Ref |
|---|---|---|---|---|---|---|---|---|
| CD | 3 | rs12714959 | 18.59–18.62 | 0.304 | 4.04e-05 | 1.51e-09 | - | Franke et al (2010) |
| 21 | rs2252931 | 33.61–33.63 | 0.266 | 3.07e-01 | 3.41e-09 | IFNGR2 | Jostins et al (2012) | |
|
| ||||||||
| BD | 6 | rs7771567 | 97.81–98.01 | 0.301 | 7.41e-12 | 1.86e-11 | MIR2113/POU3F2 | Mühleisen et al (2014) |
|
| ||||||||
| T2D | 3 | rs2377104 | 185.942570 | 0.491 | 9.57e-09 | 2.25e-09 | IGF2BP2 | Hara et al (2014) |
| 9 | rs7030479 | 4.202347 | 0.066 | 1.28e-12 | 2.26e-13 | GLIS3 | Mahajan et al (2014) | |
| 11 | rs1002227 | 17.35–17.36 | 0.302 | 3.70e-08 | 1.29e-08 | KCNJ11 | Mahajan et al (2014) | |
| 16 | rs1350889 | 81.342–81.345 | 0.478 | 4.79e-10 | 1.16e-10 | CMIP | Cho et al (2012) | |