Table 2.
Overview of the SNPs included in the pathway and enrichment analyses
| Phenotype | Locus | Chr. | SNP | A1 | F_A (%) | F_U (%) | A2 | χ2 | p-value | OR |
|---|---|---|---|---|---|---|---|---|---|---|
| IBD | U10 | 10 | rs10761659 | C | 41.40 | 49.50 | T | 11.590 | 0.000662 | 0.7212 |
| STX8 | 17 | rs9895062 | A | 4.20 | 7.80 | G | 11.180 | 0.000827 | 0.5136 | |
| C6orf85 | 6 | rs17309827 | G | 30.50 | 37.80 | T | 10.630 | 0.001115 | 0.7211 | |
| SLC22A4 | 5 | rs1050152 | C | 42.00 | 34.50 | T | 10.530 | 0.001172 | 1.3780 | |
| 5025133 | 5 | rs2522057 | C | 40.50 | 33.80 | G | 8.415 | 0.003721 | 1.3360 | |
| 5p13.1 | 5 | rs17234657 | C | 9.90 | 6.40 | T | 7.038 | 0.007979 | 1.5920 | |
| RSHL1 | 19 | rs8111071 | A | 14.30 | 10.10 | G | 7.017 | 0.008073 | 1.4880 | |
| TLR4 | 9 | rs4986790 | A | 3.50 | 5.90 | G | 6.140 | 0.013210 | 0.5776 | |
| NFATC2 | 20 | rs880324 | A | 20.00 | 24.50 | G | 5.270 | 0.021700 | 0.7704 | |
| U1 | 1 | rs17419032 | A | 19.40 | 23.80 | T | 4.760 | 0.029130 | 0.7745 | |
| STAT3 | 17 | rs744166 | C | 34.20 | 39.20 | T | 4.629 | 0.031430 | 0.8080 | |
| LYRM4 | 6 | rs12529198 | A | 8.30 | 5.80 | G | 4.361 | 0.036760 | 1.4730 | |
| NKX2-3 | 10 | rs10883365 | A | 44.40 | 49.20 | G | 3.902 | 0.048240 | 0.8248 | |
| CD | C6orf85 | 6 | rs1730982 | G | 27.90 | 37.80 | T | 15.090 | 0.000102 | 0.6366 |
| U10 | 10 | rs1076165 | C | 41.00 | 49.50 | T | 9.866 | 0.001684 | 0.7086 | |
| RSHL1 | 19 | rs8111071 | A | 15.30 | 10.10 | G | 8.528 | 0.003498 | 1.6200 | |
| 5p13.1 | 5 | rs1723465 | C | 10.70 | 6.40 | T | 8.391 | 0.003771 | 1.7400 | |
| SLC22A4 | 5 | rs1050152 | C | 42.00 | 34.50 | T | 8.090 | 0.004450 | 1.3760 | |
| 5025133 | 5 | rs2522057 | C | 41.20 | 33.80 | G | 7.692 | 0.005547 | 1.3710 | |
| TLR4 | 9 | rs4986790 | A | 2.90 | 5.90 | G | 7.427 | 0.006427 | 0.4780 | |
| CARD15 | 16 | rs2066847 | – | 3.20 | 1.20 | C | 7.023 | 0.008045 | 2.6890 | |
| U17 | 17 | rs4362447 | C | 42.20 | 35.30 | T | 6.819 | 0.009019 | 1.3420 | |
| LYRM4 | 6 | rs1252919 | A | 9.40 | 5.80 | G | 6.813 | 0.009050 | 1.6870 | |
| STX8 | 17 | rs9895062 | A | 4.40 | 7.80 | G | 6.786 | 0.009190 | 0.5499 | |
| APG16L | 2 | rs2241880 | C | 36.10 | 42.80 | T | 5.956 | 0.014660 | 0.7575 | |
| PPARG | 16 | rs2960422 | A | 35.90 | 41.90 | G | 4.982 | 0.025610 | 0.7768 | |
| STAT3 | 17 | rs744166 | C | 33.50 | 39.20 | T | 4.696 | 0.030240 | 0.7803 | |
| PPARG | 3 | rs1801282 | A | 5.30 | 8.10 | G | 4.396 | 0.036020 | 0.6385 | |
| POU2F1 | 1 | rs2814036 | A | 2.70 | 1.20 | G | 4.299 | 0.038140 | 2.2540 | |
| ATCL8 | 1 | rs7547331 | C | 27.00 | 32.00 | T | 3.916 | 0.047840 | 0.7855 | |
| CD B1 | C6orf85 | 6 | rs17309827 | G | 27.80 | 37.80 | T | 11.860 | 0.000572 | 0.6342 |
| CARD15 | 16 | rs2066847 | – | 4.00 | 1.20 | C | 10.980 | 0.000922 | 3.4740 | |
| LYRM4 | 6 | rs12529198 | A | 10.90 | 5.80 | G | 10.340 | 0.001305 | 1.9870 | |
| POU2F1 | 1 | rs2814036 | A | 3.90 | 1.20 | G | 9.246 | 0.002360 | 3.2400 | |
| 5025133 | 5 | rs2522057 | C | 42.60 | 33.80 | G | 8.519 | 0.003515 | 1.4530 | |
| U10 | 10 | rs10761659 | C | 40.80 | 49.50 | T | 8.069 | 0.004502 | 0.7044 | |
| SLC22A4 | 5 | rs1050152 | C | 42.20 | 34.50 | T | 6.716 | 0.009557 | 1.3860 | |
| TLR4 | 9 | rs4986790 | A | 2.80 | 5.90 | G | 6.228 | 0.012570 | 0.4493 | |
| 5p13.1 | 5 | rs17234657 | C | 10.40 | 6.40 | T | 5.912 | 0.015040 | 1.6860 | |
| RSHL1 | 19 | rs8111071 | A | 14.90 | 10.10 | G | 5.777 | 0.016240 | 1.5660 | |
| ATCL8 | 1 | rs7547331 | C | 25.50 | 32.00 | T | 5.005 | 0.025280 | 0.7286 | |
| U7 | 7 | rs1558043 | C | 12.80 | 17.90 | G | 4.948 | 0.026120 | 0.6744 | |
| NKX2-3 | 10 | rs7081330 | A | 40.10 | 33.60 | G | 4.944 | 0.026180 | 1.3220 | |
| U13 | 13 | rs11617463 | A | 8.90 | 5.80 | C | 4.202 | 0.040370 | 1.6040 | |
| STX8 | 17 | rs9895062 | A | 4.70 | 7.80 | G | 4.102 | 0.042830 | 0.5901 | |
| CD B2 | APG16L | 2 | rs2241880 | C | 32.00 | 42.80 | T | 6.000 | 0.014310 | 0.6299 |
| PPARG | 3 | rs1801282 | A | 2.90 | 8.10 | G | 5.620 | 0.017760 | 0.3433 | |
| C6orf85 | 6 | rs17309827 | G | 28.30 | 37.80 | T | 5.008 | 0.025230 | 0.6488 | |
| U17 | 17 | rs4362447 | C | 44.70 | 35.30 | T | 4.893 | 0.026970 | 1.4860 | |
| 5p13.1 | 5 | rs17234657 | C | 11.40 | 6.40 | T | 4.854 | 0.027580 | 1.8670 | |
| FLJ44299 | 16 | rs8050910 | G | 25.70 | 34.90 | T | 4.606 | 0.031860 | 0.6455 | |
| NKX2-3 | 10 | rs10883365 | A | 39.60 | 49.20 | G | 4.502 | 0.033860 | 0.6761 | |
| U10 | 10 | rs10761659 | C | 40.00 | 49.50 | T | 4.302 | 0.038060 | 0.6802 | |
| PPARG | 16 | rs2960422 | A | 32.90 | 41.90 | G | 4.277 | 0.038630 | 0.6796 | |
| CD B3 | RSHL1 | 19 | rs8111071 | A | 20.50 | 10.10 | G | 4.751 | 0.029270 | 2.3010 |
| UC | STX8 | 17 | rs9895062 | A | 3.70 | 7.80 | G | 7.447 | 0.006353 | 0.4574 |
| NFATC2 | 20 | rs880324 | A | 18.40 | 24.50 | G | 5.590 | 0.018060 | 0.6965 | |
| U10 | 10 | rs10761659 | C | 42.10 | 49.50 | T | 5.826 | 0.015790 | 0.7404 | |
| U9 | 9 | rs7869487 | C | 24.50 | 30.00 | T | 3.960 | 0.046600 | 0.7558 | |
| NKX2-3 | 10 | rs10883365 | A | 42.50 | 49.20 | G | 4.653 | 0.031000 | 0.7624 | |
| 5025133 | 5 | rs2522057 | C | 39.70 | 33.80 | G | 3.929 | 0.047470 | 1.2870 | |
| SLC22A4 | 5 | rs1050152 | C | 42.10 | 34.50 | T | 6.536 | 0.010570 | 1.3820 | |
| CDKAL1 | 6 | rs6908425 | C | 23.10 | 17.00 | T | 6.567 | 0.010390 | 1.4720 | |
| UC E1 | U3 | 3 | rs1462651 | C | 19.40 | 9.00 | T | 8.134 | 0.004345 | 2.4400 |
| 5p13.1 | 5 | rs17234657 | C | 14.30 | 6.40 | T | 6.064 | 0.013800 | 2.4200 | |
| NCF4 | 22 | rs4821544 | C | 52.90 | 38.00 | T | 5.833 | 0.015730 | 1.8340 | |
| DLG5 | 10 | rs1248696 | C | 0.00 | 7.40 | T | 5.538 | 0.018610 | 0.0000 | |
| CYLD | 16 | rs17223195 | A | 27.00 | 40.90 | G | 5.444 | 0.019640 | 0.5352 | |
| U13 | 13 | rs11617463 | A | 12.50 | 5.80 | C | 5.087 | 0.024100 | 2.3370 | |
| U10 | 10 | rs6601764 | C | 56.90 | 44.10 | T | 4.421 | 0.035510 | 1.6790 | |
| UC E2 | STX8 | 17 | rs9895062 | A | 2.80 | 7.80 | G | 4.551 | 0.032910 | 0.3438 |
| CDKAL1 | 6 | rs6908425 | C | 23.90 | 17.00 | T | 3.894 | 0.048450 | 1.5400 | |
| UC E3 | NKX2-3 | 10 | rs10883365 | A | 37.90 | 49.20 | G | 7.531 | 0.006065 | 0.6302 |
| 5p13.1 | 5 | rs1992660 | C | 28.80 | 38.30 | T | 5.832 | 0.015730 | 0.6513 | |
| PGLYRP4 | 1 | rs10888557 | C | 19.80 | 13.00 | G | 5.823 | 0.015820 | 1.6510 | |
| 5025133 | 5 | rs2522057 | C | 43.10 | 33.80 | G | 5.715 | 0.016820 | 1.4830 | |
| U10 | 10 | rs10761659 | C | 40.00 | 49.50 | T | 5.546 | 0.018520 | 0.6802 | |
| FLJ45139 | 21 | rs2836753 | C | 47.80 | 38.40 | T | 5.448 | 0.019590 | 1.4690 | |
| SLC22A4 | 5 | rs1050152 | C | 43.50 | 34.50 | T | 5.249 | 0.021960 | 1.4620 | |
| STX8 | 17 | rs9895062 | A | 3.20 | 7.80 | G | 4.997 | 0.025390 | 0.3910 | |
| C6orf85 | 6 | rs17309827 | G | 29.20 | 37.80 | T | 4.657 | 0.030930 | 0.6787 | |
| 5p13.1 | 5 | rs9292777 | C | 32.10 | 40.60 | T | 4.575 | 0.032440 | 0.6901 | |
| FAF1 | 1 | rs11205760 | C | 19.50 | 26.90 | T | 4.460 | 0.034700 | 0.6567 | |
| FLJ45139 | 12 | rs2836754 | C | 48.90 | 40.50 | T | 4.408 | 0.035770 | 1.4070 | |
| NFATC2 | 20 | rs880324 | A | 17.60 | 24.50 | G | 4.126 | 0.042240 | 0.6561 |
The columns from left to right are: phenotype (disease and sub-phenotypes), locus, chromosome, SNP, allele 1 base, frequency of allele 1 in affected individuals, frequency of allele 1 in unaffected individuals, allele 2 base, the score of the basic allelic test χ2 (1 df), asymptotic p-value for this test and, estimated odds ratio for allele 1