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Table 3 Vitamin C versus Placebo DMCs located within DMRs and associated with expression levels of mRNA

From: Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes

Probe ID and location

eQTM

Mean across DMR

Probe

Nearest gene

Chr

Start

Genomic region

Ensembl GeneId

RNA-seq GeneName

Coeff

SE

P value

FDR adj.P.Val

∆β PN

∆β VP

% Restored

cg08757348

ZNF214

11

7041565

5'UTR-island

ENSG00000149054

ZNF215

− 50.90

6.34

1.77E−11

8.12E−08

0.00

0.00

− 274.61

cg10885961

LINC00667

18

5238589

Body-island

ENSG00000263753

LINC00667

− 2.20

0.33

3.56E−09

5.44E−06

0.01

− 0.08

542.67

cg00684824

COL21A1

6

56112024

5'UTR-shore

ENSG00000124749

COL21A1

2.89

0.46

2.70E−08

3.10E−05

0.02

− 0.05

255.48

cg00433866

MOG

6

29623646

TSS1500-opensea

ENSG00000204644

ZFP57

15.20

2.47

4.14E−08

3.76E−05

− 0.04

0.06

136.70

cg04395593

C9orf106

9

132044732

Body-opensea

ENSG00000224307

AL161785.1

− 2.44

0.41

7.18E−08

4.12E−05

0.04

− 0.08

180.49

cg21175940

RNF39

6

30038910

Body-island

ENSG00000204618

RNF39

23.58

4.28

5.72E−07

1.88E−04

0.00

− 0.01

− 230.29

cg14948785

NLRP14

11

7041870

1stExon-island

ENSG00000149054

ZNF215

− 47.35

8.76

8.81E−07

2.70E−04

0.00

0.00

− 192.77

cg24384195

PIK3CG

7

106505370

TSS1500-shelf

ENSG00000105851

PIK3CG

− 9.05

1.68

9.86E−07

2.83E−04

0.00

0.01

− 146.10

cg22384902

SND1

7

127671261

TSS1500-island

ENSG00000128594

LRRC4

− 5.64

1.08

1.66E−06

4.23E−04

0.02

− 0.02

84.88

cg07652350

IRF7

11

616009

TSS1500-island

ENSG00000185507

IRF7

− 1.53

0.30

2.92E−06

6.30E−04

0.03

− 0.06

196.36

cg02378269

IVD

15

40697591

TSS200-shore

ENSG00000128928

IVD

− 0.97

0.20

7.74E−06

1.27E−03

− 0.05

0.05

100.42

cg04328729

DIP2C

10

521830

Body-shelf

ENSG00000151240

DIP2C

2.06

0.44

1.12E−05

1.56E−03

− 0.01

− 0.03

− 294.15

cg08201311

OBSL1

2

220435003

1stExon-island

ENSG00000124006

OBSL1

− 1.83

0.40

2.31E−05

2.74E−03

− 0.01

− 0.06

− 526.37

cg11479689

NRL

14

24563183

TSS1500-shore

ENSG00000100889

PCK2

− 1.10

0.25

3.04E−05

3.37E−03

− 0.09

0.06

68.11

cg15467148

PCK2

14

24563578

1stExon-island

ENSG00000100889

PCK2

− 1.26

0.28

3.26E−05

3.49E−03

− 0.08

0.06

82.03

cg06173720

LRRC4

7

127670993

5'UTR-shore

ENSG00000128594

LRRC4

− 6.02

1.40

5.26E−05

4.66E−03

0.01

− 0.01

87.33

cg23370394

BAHCC1

17

79410470

Body-shore

ENSG00000185332

TMEM105

6.19

1.57

1.85E−04

1.21E−02

− 0.02

0.02

101.82

cg16316672

LINC00526

18

5237581

TSS1500-shore

ENSG00000264575

LINC00526

− 3.04

0.80

3.29E−04

2.07E−02

0.01

− 0.01

101.38

cg25464210

ZNF85

19

21106002

TSS200-opensea

ENSG00000105750

ZNF85

− 0.88

0.23

3.56E−04

2.18E−02

− 0.07

0.07

106.16

cg15676302

DMTN

8

21909754

TSS1500-shelf

ENSG00000208037

MIR320A

3.95

1.07

4.64E−04

2.68E−02

− 0.03

0.02

82.05

cg08092680

TCL1A

14

96181044

TSS1500-shore

ENSG00000182512

GLRX5

2.66

0.77

9.56E−04

4.93E−02

0.01

− 0.01

122.95

  1. Shown here is the top FDR significant CpG per DMR associated with expression, sorted by p value
  2. eQTM = expression quantitative trait loci. Nearest gene = nearest proximal gene using the chromosome and positions (GrCh37/hg19) provided for each probe in the Illumina HumanMethylationEPIC annotation file, matched to the nearest gene symbol using the GenomicRanges package in R; Chr = Chromosome; Start = Position (hg19); Ensembl GeneId = associated transcript within ± 250 kb of the CpG site; RNA-seq GeneName = annotated to Ensembl with Biomart; Coeff = coefficient from eQTM association; SE = standard error; ∆β PN = delta beta placebo versus nonsmokers; ∆β VP = delta beta vitamin C versus placebo smokers; percent restored = (− ∆β VP/∆β PN) * 100
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Clinical Epigenetics

ISSN: 1868-7083

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