Table 4 Validation of differentially methylated genetic loci in the genome-wide methylation analysis of Crohn’s disease and ulcerative colitis

From: Altered DNA methylation within DNMT3A, AHRR, LTA/TNF loci mediates the effect of smoking on inflammatory bowel disease

Outcome

Gene

Genome-wide methylation analysis

CpG site

Region

beta

se

P-value

FDR

Crohn’s disease

LTA

cg16280132

5’UTR

0.009

0.004

3.43 × 10−2

4.49 × 10−2

 

DNMT3A

cg23393100

body

0.002

0.001

1.46 × 10−2

3.40 × 10−2

 

cg17207266

body

0.008

0.002

4.36 × 10−5

1.42 × 10−3

 

cg05544807

body

0.012

0.003

2.77 × 10−4

3.61 × 10−3

 

cg20702417

body

0.010

0.003

7.66 × 10−4

7.11 × 10−3

 

cg03314052

body

0.008

0.003

1.69 × 10−2

3.43 × 10−2

 

cg11779362

body

0.002

0.001

1.03 × 10−2

3.04 × 10−2

 

HIVEP3

cg00970057

body

0.009

0.003

3.59 × 10−3

1.56 × 10−2

 

cg09501963

body

0.005

0.002

2.83 × 10−2

4.34 × 10−2

 

cg24051040

body

0.004

0.002

3.87 × 10−2

4.49 × 10−2

 

HNRNPF

cg00326958

5’UTR

−0.007

0.003

8.06 × 10−3

3.00 × 10−2

 

MACROD1

cg10612274

body

0.025

0.007

2.06 × 10−4

3.35 × 10−3

 

cg17590162

body

0.013

0.005

1.30 × 10−2

3.20 × 10−2

 

cg12424921

body

0.010

0.005

2.84 × 10−2

4.34 × 10−2

 

cg04582871

body

0.011

0.005

3.77 × 10−2

4.49 × 10−2

 

cg09908110

body

0.001

0.001

4.56 × 10−2

4.69 × 10−2

 

cg09375205

body

0.006

0.002

1.56 × 10−2

3.43 × 10−2

 

cg02374207

body

0.002

0.001

1.12 × 10−2

3.12 × 10−2

Ulcerative colitis

AHRR

cg22356527

body

−0.005

0.002

3.04 × 10−2

4.47 × 10−2

 

cg19602050

body

−0.001

0.000

1.72 × 10−2

3.59 × 10−2

 

cg12806681

body

0.006

0.002

5.53 × 10−3

2.71 × 10−2

 

cg02088390

body

−0.002

0.001

2.33 × 10−2

4.37 × 10−2

 

cg26703534

body

0.013

0.004

1.22 × 10−3

1.25 × 10−2

 

cg11894422

body

0.005

0.002

3.21 × 10−2

4.47 × 10−2

 

cg21161138

body

0.013

0.004

3.52 × 10−3

2.16 × 10−2

 

cg23576855

body

0.034

0.016

3.71 × 10−2

4.47 × 10−2

 

cg11557553

body

−0.004

0.002

4.66 × 10−2

4.87 × 10−2

 

cg25648203

body

0.010

0.004

1.51 × 10−2

3.42 × 10−2

 

DNMT3A

cg26544247

body

0.006

0.003

3.71 × 10−2

4.47 × 10−2

 

cg20702417

body

0.006

0.003

4.85 × 10−2

4.93 × 10−2

 

cg15843262

body

0.005

0.002

5.10 × 10−3

2.65 × 10−2

 

cg17207266

body

0.006

0.002

4.35 × 10−3

2.45 × 10−2

 

cg27369452

body

0.001

0.001

8.24 × 10−3

3.05 × 10−2

 

cg05544807

body

0.009

0.003

2.81 × 10−3

2.00 × 10−2

 

cg11779362

body

0.002

0.001

4.91 × 10−2

4.93 × 10−2

  1. Gene names are italicized. These loci were validated by a genome-wide DNA methylation analysis of inflammatory bowel disease11. All tests were two-sided and adjusted for multiple comparisons.
  2. 5’UTR 5ʹ untranslated region, Body Gene body, FDR false discovery rate.
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