Table 1.
G×G (SNP×SNP) interaction between WNT genes and CL/P GWAS genes: Most significant results of the conditional logistic regression epistatic test and corresponding case-only test results for the top ranked SNPs from Random Forests analysis and CL/P GWAS significant SNPs (SNPs pruned to have r2 < 0.1)
| Gene1 | Gene2 | SNP1 (CHR) | SNP2 (CHR) | Case-only test P-value | Epistatic test P-value In Asians | Epistatic test P-value In Europeans |
|---|---|---|---|---|---|---|
| Asian | ||||||
| WNT5B | MAFB | rs4765835 (chr12) | rs11696257 (chr20) | P = 0.7237 (P = 0.00078)a | 0.0085* Empiric P** = 0.0076* |
0.017† Empiric P** = 0.018† |
| WNT2 | IRF6 | rs2023708 (chr7) | rs1044516 (chr1) | P = 0.023 | 0.019† | 0.65 |
| WNT2 | ABCA4 | rs2023708 (chr7) | rs6686599 (chr1) | P = 0.012 | 0.015† | 0.29 |
| European | ||||||
| WNT5A | ABCA4 | rs1499890 (chr3) | rs3789451 (chr1) | P = 0.03 | 0.84 | 0.037† |
| WNT4 | MAFB | rs2807376 (chr1) | rs13041247 (chr20) | P = 0.017 | 0.44 | 0.044† |
| FILIP1L | chr8q24 | rs813218 (chr3) | rs12546523 (chr8) | P = 0.017 | 0.19 | 0.0011* Empiric P** = 0.0017* |
*
P-value < 0.01
†
P-value < 0.05
**
Empiric P value used 10,000 permutations.
a
In Asian trios using the case-only test, rs4765835 and rs11696257 did not show evidence of interaction (P = 0.7237) but rs4765835 showed strong evidence of interaction with another SNP in MAFB, rs6102085 (P = 0.00078).