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Table 3 Differentially methylated regions in blood DNA in relation to current smoking compared to never smoking (multiple-testing corrected p < 0.01 at DMRcate and comb-p, ordered by chromosomal location)

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

Chra

Gene

Distance to geneb

DMRcate

Comb-p

Minimum P i

Start (bpc)

End (bp)

FDRd

#CpGse

Start (bp)

End (bp)

Sidak Pf

#CpGs

1

MXRA8

−812

1286917

1287259

0.002

2(2)

  

0.002

 

2.2E−04

CASZ1

−600

10695686

10696066

8.7E−04

2(2)

  

0.009

 

1.5E−05

AHDC1

 

27929092

27929260

2.2E−04

2(2)

  

0.006

 

1.5E−04

NT5C1A

 

40137636g

40138402

3.2E−06

6(3)

  

0.001

 

5.5E−06

ACOT11 h

−58,441

54954187

54955366

0.002

7(4)

54953632

 

0.009

8(4)

6.1E−04

GNG12 h

 

68298816g

68299511

7.0E−07

7(5)

68299057

 

0.001

6(5)

1.4E−06

GFI1 h

 

92946700

92947961

1.1E−04

6(4)

  

1.2E−04

 

8.1E−05

SPAG17

 

118727658g

118728226

1.3E−04

10(2)

  

0.005

 

7.1E−06

ZNF697

 

120173989

120174570

0.006

4(4)

 

120174873

0.006

6(4)

0.002

GALNT2

 

230415343

230416101

0.002

6(3)

230414987

230417096

1.2E−04

12(4)

0.005

SCCPDH

−26,962

246859889

246860416

7.0E−04

5(4)

  

2.6E−04

 

0.002

2

PAX8

 

113992762

113993313

0.005

8(6)

  

0.004

 

0.011

ALPPL2 h

11,458

233283010g

233285607

8.0E−15

8(5)

  

1.5E−13

 

8.4E−09

SNED1 h

 

241975756

241976244

1.9E−06

4(4)

  

3.8E−06

 

1.4E−04

3

KRBOX1

11

42977777

42978180

9.7E−04

7(5)

  

0.003

 

4.1E−04

GPR15 h

 

98250723g

98251294

6.2E−07

2(1)

98249859

 

6.2E−04

4(2)

1.0E−07

ZBTB38

 

141086820

141087363

0.006

6(4)

  

0.005

 

0.005

LPP h

 

187870621

187871538

1.5E−05

11(5)

  

0.001

 

1.1E−04

C3orf43

21,882

196255632

196256223

9.7E−04

5(3)

  

0.004

 

1.8E−04

4

PCGF3

 

737005

738199

0.002

8(2)

736328

 

0.001

12(4)

2.5E−05

FGFRL1

−1776

1003208

1003834

1.5E−04

3(2)

  

0.002

 

2.0E−04

PRDM8

 

81117647g

81119473

6.7E−13

11(10)

  

2.9E−13

 

6.7E−06

NHEDC1

 

103940711

103941300

6.8E−14

11(10)

  

2.7E−10

 

6.2E−05

CFI

 

110724358

110724834

0.006

2(2)

  

0.009

 

4.4E−04

5

AHRR h

 

373378g

374425

4.6E−17

5(2)

 

373887

4.8E−05

2(1)

6.5E−13

392920g

393366

5.8E−08

3(3)

  

3.9E−08

 

4.7E−06

LPCAT1

 

1494980

1495356

0.001

5(4)

  

0.003

 

0.001

LINC01019

−236,319

3180918

3180947

0.006

2(2)

 

3182108

6.0E−04

5(4)

5.7E−04

FLJ44606

 

126408756

126409553

7.0E−07

13(11)

  

1.9E−06

 

0.001

ADAMTS2

 

178548229

178548700

0.002

3(3)

  

0.003

 

8.5E−04

6

IER3 h

9104

30720080

30720491

1.2E−06

8(4)

  

0.002

 

1.7E−05

LY6G6E

 

31683051

31683352

5.4E−05

6(5)

  

1.2E−04

 

0.002

HLA-DPB1

 

33047944

33049505

2.5E−09

20(15)

  

4.8E−08

 

0.002

SYNGAP1 h

 

33400477

33401542

6.9E−06

9(7)

33400021

 

2.2E−05

10(7)

2.7E−04

CRISP2

 

49681178

49681774

5.5E−06

9(8)

  

5.5E−06

 

1.8E−04

UTRN

−4373

144607399

144608500

0.004

7(4)

144607074

 

0.010

8(4)

2.6E−04

ZC3H12D h

 

149805995

149806732

2.3E−15

10(10)

  

1.9E−14

 

8.7E−05

TIAM2 h

 

155537595

155538155

1.6E−05

8(5)

  

3.7E−05

 

7.6E−04

THBS2

 

169653612

169654719

9.5E−04

11(4)

 

169654842

7.0E−04

12(4)

5.3E−04

7

GNA12 h

 

2768988

2770410

4.7E−06

5(5)

2769253

 

7.4E−05

4(4)

3.0E−05

TRG-AS1 h

−29,710

38350464

38351468

2.0E−06

7(6)

  

1.1E−05

 

1.7E−04

MYO1G h

 

45001765g

45002919

5.5E−14

6(5)

  

5.7E−09

 

2.7E−06

INSIG1

61,195

155150681

155151427

0.007

4(3)

  

0.002

 

0.003

8

DEFA4

 

6795162

6796618

2.0E−04

4(4)

6794872

 

1.7E−05

5(4)

4.0E−05

EPB49 h

 

21915184

21915510

0.004

2(2)

21914287

21916853

5.3E−05

11(6)

0.002

TRAPPC9

 

141057285

141057827

3.7E−06

5(5)

  

2.1E−06

 

2.0E−04

GLI4

 

144358043

144359316

0.001

5(5)

  

1.5E−05

 

0.002

9

CD72

 

35609853

35610380

0.002

2(2)

  

0.007

 

1.1E−04

CIZ1

 

130955135

130956057

0.001

4(3)

 

130955436

0.004

3(3)

0.001

10

SNCG

 

88717926

88718393

5.5E−04

5(5)

  

3.8E−04

 

0.003

SLC16A12 h

 

91296252

91296457

1.6E−04

3(3)

  

0.004

 

4.4E−04

LGI1

 

95517382

95517895

6.3E−04

7(4)

  

0.002

 

5.6E−04

NKX2-3

−4844

101287381g

101287846

8.2E−06

5(3)

  

1.3E−04

 

7.4E−06

GRK5

 

121171859

121172898

6.4E−04

5(4)

  

2.4E−04

 

4.1E−04

11

C11orf21 h

 

2321770

2322674

1.2E−05

18(7)

 

2323938

1.3E−04

33(8)

5.9E−04

C11orf41

 

33562503

33563377

7.0E−04

4(4)

 

33563946

2.3E−04

5(4)

5.4E−04

NEAT1 h

4664

65194933

65196227

2.2E−05

7(7)

 

65196696

3.0E−05

10(7)

4.9E−04

ACY3

 

67418045

67418405

1.1E−09

12(11)

  

8.7E−08

 

1.3E−04

CCND1

 

69462660g

69463323

2.4E−06

6(3)

  

1.7E−04

 

7.5E−07

AMICA1 h

 

118084920

118085736

0.005

4(4)

  

0.002

 

0.003

12

IFFO1

 

6657744

6658945

2.7E−04

10(5)

 

6659524

2.2E−04

12(5)

8.1E−05

MGP

 

15038440

15039432

9.5E−04

4(3)

  

3.5E−05

 

9.3E−05

KRT7

 

52638005

52638592

0.002

3(2)

  

0.005

 

1.5E−04

ZNF385A

 

54778312

54779175

0.002

4(3)

  

0.008

 

0.001

RP11-474D1.3

36,620

130554977

130555091

1.8E−04

3(3)

  

9.4E−04

 

1.7E−04

STX2

−73,033

131199848

131201112

7.2E−04

10(4)

131198873

131201268

0.008

12(5)

6.5E−05

14

LGMN

 

93170710

93170970

0.002

3(3)

  

0.008

 

6.6E−05

EVL

 

100610071

100610667

9.8E−05

6(4)

  

1.9E−04

 

4.0E−04

RIN3

 

92981121

92981666

1.6E−05

3(3)

  

2.1E−05

 

1.8E−04

15

CALML4

 

68498251g

68499367

2.6E−06

5(2)

68497992

 

0.002

6(2)

2.9E−07

16

PRR25

 

854168

854640

0.002

4(3)

 

855449

0.002

6(4)

7.7E−04

BCL7C

 

30906810

30907246

0.001

2(2)

 

30907560

8.0E−04

3(3)

9.0E−04

17

ALOX15B

 

7942137

7942743

1.1E−04

6(5)

  

2.4E−04

 

3.9E−04

NTN1

 

9018806

9019336

2.0E−05

5(4)

  

5.5E−04

 

5.3E−04

SLFN12L

−13,916

33787402

33788026

0.003

4(4)

  

0.001

 

8.8E−04

CYB561

 

61511069

61511829

4.9E−04

4(4)

  

9.3E−05

 

5.2E−04

CCDC57

 

80076338

80076378

1.1E−04

2(2)

  

0.002

 

2.2E−05

FOXK2

 

80545020g

80545869

8.1E−08

11(6)

  

2.6E−04

 

5.5E−06

TBCD

 

80870107

80870923

0.001

5(3)

 

80871405

0.002

7(4)

1.8E−04

18

C18orf1

 

13611370

13611824

0.007

6(4)

  

0.009

 

0.003

19

GNG7

 

2543602

2544100

0.008

5(2)

2542837

 

0.002

6(3)

6.4E−04

MAN2B1

 

12758416

12759546

0.004

7(4)

  

0.001

 

0.002

LAIR1

 

54876446

54876795

1.8E−04

5(4)

  

8.1E−04

 

2.3E−04

20

C20orf27

 

3745817

3746315

0.002

2(2)

  

0.004

 

8.8E−05

22

SYNGR1

 

39759864g

39760267

1.2E−07

5(5)

  

1.2E−06

 

2.5E−06

SHISA8

−978

42304331

42304580

1.4E−04

2(2)

  

6.9E−04

 

2.3E−05

ODF3B

 

50970943

50971140

4.2E−04

3(3)

  

0.002

 

1.6E−04

  1. Empty cells in “Start,” “End,” and “#CpGs” for comb-p represent the same regional information compare to results in DMRcate. DMRs ordered by p values can be found in Additional file 11
  2. aChromosome
  3. bMinimum distance to transcription start site of the mapped gene (basepair)
  4. cPhysical position (basepair, National Center for Biotechnology Information human reference genome assembly Build 37.3)
  5. dFalse discovery rate
  6. eNumber of probes in the region (number of CpGs of nominal statistical significance)
  7. f P of Sidak multiple-testing correction
  8. gRegion including significant (FDR <0.05) differentially methylated probes from our epigenome-wide association study (EWAS)
  9. hGene identified in previous EWASs of smoking
  10. iMinimum p values among unadjusted p values of CpGs in each region