Skip to main content

Table 2 Overview of the SNPs included in the pathway and enrichment analyses

From: Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

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
  1. 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