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Table 5 Differential methylation in relation to current smoking for genes with transcripts differently expressed (p < 0.05) in relation to smoking pack-years (ordered by chromosomal location)

From: DNA methylation and smoking in Korean adults: epigenome-wide association study

Differentially methylated probes in relation to current smoking compared to never smoking (the Korean COPD cohort)

Gene (distance to genec)

Differentially expressed genes in relation to pack-years in lung tissue (Asan Biobank)

Differentially methylated probe

  

 Chra

Probe

Coef b

P

Genomic features

CpG island

 

Transcript

Coef

P

  1

cg20388635

−0.013

1.3E−05

TSS200, promoter

Island

YTHDF2

NM_001173128

−0.019

0.047

  2

cg22346073

−0.056

5.1E−08

5′UTR

Shelf

CLASP1

NM_015282

0.019

7.2E−04

cg19394739

−0.012

3.5E−07

Body, promoter

Shore

DGUOK

NM_080916

−0.079

0.003

cg09059267

−0.099

4.2E−06

 

Island

DNPEP (−15098)

NM_012100

−0.021

0.037

  3

cg01870865

−0.045

1.0E−05

TSS200, promoter

 

TREX1

NM_033629

−0.018

0.023

cg19859270d

−0.027

1.0E−07

1st exon

 

GPR15 e

NM_005290

0.013

3.0E−04

  5

cg05575921d

−0.203

6.5E−13

Body, enhancer

Shore

AHRR e

NM_001242412

0.004

0.047

cg14817490d

−0.078

4.7E−06

Body, promoter, DHS

 

cg25648203d

−0.079

6.2E−07

Body, enhancer, DHS

 

  6

cg23164938

−0.016

9.5E−06

TSS1500

Shore

ESR1

NM_000125

0.005

0.012

  7

cg05383910

−0.042

2.1E−06

5′UTR, enhancer

 

ELMO1 e

NR_038121

0.017

0.031

cg20663219

−0.054

9.4E−06

Body, DHS

Shelf

STX1A

NM_001165903

−0.003

0.045

  10

cg20723792

−0.097

4.8E−10

Body, enhancer, DHS

 

FAM53B

NM_014661

0.009

0.042

  11

cg25426350

−0.030

2.5E−06

TSS200

 

HPX

NM_000613

−0.003

0.024

  13

cg17058676

−0.028

2.5E−06

Body

Shore

CENPJ

NM_018451

0.003

0.035

  14

cg16579351

−0.017

1.2E−05

Body

 

BRF1

NM_001242788

−0.012

0.041

  17

cg13521620

−0.052

1.2E−05

5′UTR

Shore

YPEL2

NM_001005404

0.019

0.023

Differentially methylated region

    

 Chr

Region

#CpGs

FDR

Genomic features

CpG island

    

  1

230415343–230416101

6

0.002

3′UTR

Island, shore

GALNT2

NM_004481

0.033

0.018

  2

241975756–241976244

4

1.9E−06

Body, promoter, DHS

island

SNED1 e

NM_001080437

0.017

0.014

  3

98250723–98251294

2

6.2E−07

TSS200, 1st exon

 

GPR15 e

NM_005290

0.013

3.0E−04

  3

187870621–187871538

11

1.5E−05

TSS1500, TSS200

Shore, island

LPP e

NM_005578

0.019

0.018

  5

373378–374425

5

4.6E−17

Body, enhancer

Shore, island

AHRR e

NM_001242412

0.004

0.047

  5

392920–393366

3

5.8E−08

Body, promoter, DHS

 

  7

2768988–2770410

5

4.7E−06

3′UTR, enhancer

 

GNA12 e

NM_007353

0.022

0.019

  17

61511069–61511829

4

4.9E−04

3′UTR, body, enhancer

Shore, island

CYB561

NM_001017916

−0.056

0.005

  1. Genomic features were based on Illumina’s Annotation file and those for DMRs were based on CpGs at start and end position of each region. Categories for the features includes (1) Body, gene body; (2) 5′UTR, 5 prime untranslated region; (3) 3′UTR, 3 prime untranslated region; (4) TSS200, 200 basepair within transcription start site; (5) TSS1500, 1500 basepair within transcription start site; and (6) DHS, DNase I hypersensitivity site
  2. aChromosome
  3. bRegression coefficient from statistical model
  4. cDistance to transcription start site of the mapped gene (basepair, National Center for Biotechnology Information human reference genome assembly Build 37.3)
  5. dProbe identified in previous epigenome-wide association studies (EWASs) of smoking
  6. eGene identified in previous EWASs of smoking