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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