Table 2. Genes Identified by Pathway Analysis for the Top 23 Meta-Analysis Loci.
| Chr | SNP | Meta p-value | GRAIL gene | GRAIL p-pvalue | DAPPLE2 gene | DAPPLE2 p-value | PrixFixe gene | PrixFixe GA score | VEGAS2 gene | VEGAS2 p-value |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | rs896319 | 1.08x10-6 | RIPK5, TMCC2 | 1 | NUAK2 | 0.072 | CNTN2 | 0.48 | DSTYK | 1.31x10-4 |
| 2 | rs12612573 | 3.86x10-6 | SCN7A | 0.184 | NA | NA | SCN7A | 0.14 | SCN7A | 6.30x10-5 |
| 3 | rs12493910 | 3.14x10-6 | ERC2 | 0.604 | ERC2 | NA | WNT5A | 0.62 | ERC2 | 0.016 |
| 4 | rs59885791 | 3.06x10-7 | KDR | 0.307 | KDR | 0.488 | KDR | 0.47 | KDR | 0.178 |
| 6 | rs11155615 | 1.57x10-6 | UST | 0.588 | NA | NA | TAB2 | 0.35 | UST | 0.005 |
| 7 | rs17171229 | 1.11x10-28 | SFRP4 | 0.001 | SFRP4 | 0.236 | SFRP4 | 0.59 | SFRP4, EPDR1, NME8 | 1.00x10-6 |
| 8 | rs1485748 | 1.76x10-6 | EBF2 | 0.285 | NA | NA | BNIP3L | 0.21 | EBF2 | 0.005 |
| 8 | rs13279808 | 1.02x10-10 | NA | NA | NA | NA | SULF1 | 0.36 | LOC100505718 | 1.00x10-6 |
| 8 | rs422847 | 9.29x10-9 | RSPO2 | 0.001 | NA | NA | EIF3E | 0.22 | EIF3E | 2.00x10-6 |
| 8 | rs183228744 | 7.85x10-6 | SCXB | 0.014 | FBXL6 | 0.311 | SCRIB | 0.47 | SCXB | 1.02x10-4 |
| 9 | rs7867335 | 6.24x10-9 | NA | NA | NA | NA | NA | NA | DMRT2 | 0.569 |
| 9 | rs28436028 | 3.58x10-6 | FBP1 | 0.531 | FBP2 | 0.429 | FBP2 | 0.19 | FBP1 | 0.002 |
| 10 | rs138852017 | 8.04x10-6 | NA | NA | NA | NA | KLF6 | 0.16 | MIR6078 | 0.019 |
| 10 | rs10786118 | 2.35x10-6 | NA | NA | NA | NA | NA | NA | DYDC2 | 0.007 |
| 10 | rs61862987 | 3.71x10-6 | TCERG1L | 0.718 | NA | NA | NA | NA | TCERG1L | 0.477 |
| 11 | rs661148 | 1.78x10-6 | GRIA4 | 1 | GRIA4 | 0.260 | AASDHPPT | 0.12 | GRIA4 | 2.44x10-4 |
| 15 | rs12899214 | 9.02x10-6 | NA | NA | SMAD3 | 0.522 | SMAD3 | 0.46 | SMAD3 | 0.041 |
| 15 | rs4932195 | 1.02x10-7 | NA | NA | ACAN | NA | ACAN | 0.40 | ISG20 | 1.00x10-6 |
| 16 | rs7189020 | 7.03x10-6 | AXIN1 | 0.007 | PDIA2 | 0.082 | AXIN1 | 0.54 | LUC7L | 1.60x10-6 |
| 16 | rs184572725 | 6.26x10-6 | CACNA1H | 0.559 | TPSAB1 | 0.135 | NA | NA | TPSD1 | 0.052 |
| 19 | rs60333289 | 1.37x10-10 | ZNF264 | 0.434 | AURKC | NA | ZIM2 | 0.31 | ZNF264 | 2.00x10-6 |
| 20 | rs3577 | 1.12x10-7 | MAFB | 0.006 | MAFB | 0.591 | PLCG1 | 0.53 | MAFB | 3.16x10-4 |
| 22 | rs28502139 | 1.75x10-16 | WNT7B | 0.001 | WNT7B | 0.095 | WNT7B | 0.60 | WNT7B, LOC730668, LINC00899, PRR34, LOC150381, MIRLET7BHG, MIR3619 | 1.00x10-6 |
Candidate genes identified by three different pathway tools, GRAIL, DAPPLE2 and PrixFixe, and the gene-based test with VEGAior the 23 meta-analysis loci.
NA–no data available (no candidate gene found).