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Table 3 Genome-wide scan of DNA methylation for an association with fasting level of HOMA-IR (as a continuous variable)

From: DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer

Chr

CpG site§

Position

Discovery

Validation

Meta-analysis

CpG context

Gene

Gene region

Effect† (95% CI)

Effect (95% CI)

p

Effect (95% CI)

p

pQÂ¥

chr1

cg05399785

3,564,031

3.32 (2.22, 4.43)

1.20 (− 3.08, 5.48)

0.578

3.19 (2.12, 4.25)

4.70E-09

0.339

N Shelf

WDR8

Body

chr1

cg09823288

239,552,128

− 1.52 (− 2.02, − 1.02)

− 3.51 (− 5.47, -1.56)

0.001

− 1.64 (− 2.13, − 1.16)

1.93E− 11

0.050

S Shore

 

Intergenic

chr1

cg11832534

3,563,998

3.84 (2.47, 5.21)

2.30 (− 2.18, 6.78)

0.311

3.70 (2.40, 5.01)

2.67E-08

0.513

N Shelf

WDR8

Body

chr1

cg14476101

120,255,992

− 1.77 (− 2.25, − 1.30)

− 3.73 (− 5.65, − 1.80)

0.0002

− 1.89 (− 2.35, − 1.43)

1.08E-15

0.050

S Shore

PHGDH

Body

chr1

cg16246545

120,255,941

− 1.91 (− 2.54, − 1.28)

− 3.01 (− 5.39, − 0.63)

0.014

− 1.99 (− 2.60, − 1.38)

1.77E-10

0.374

S Shore

PHGDH

Body

chr1

cg16395997

3,562,798

2.18 (1.39, 2.96)

2.45 (− 0.54, 5.44)

0.107

2.19 (1.43, 2.95)

1.60E-08

0.860

S Shore

WDR8

Body

chr1

cg17901584*

55,353,706

− 2.22 (− 2.94, − 1.49)

− 3.01 (− 5.66, − 0.36)

0.027

− 2.27 (− 2.97, − 1.58)

1.85E-10

0.568

S Shore

DHCR24

TSS1500

chr1

cg19693031

145,441,552

− 2.66 (-3.26, − 2.07)

− 4.49 (− 6.37, − 2.62)

 < 0.001

− 2.83 (− 3.40, − 2.27)

9.98E-23

0.065

OpenSea

TXNIP

3'UTR

chr2

cg00391067

39,145,400

2.93 (1.86, 4.01)

4.25 (0.07, 8.43)

0.046

3.02 (1.98, 4.05)

1.20E-08

0.544

OpenSea

LOC100271715

TSS1500

chr3

cg27275941**

15,751,015

− 2.10 (− 2.89, − 1.31)

− 0.55 (− 3.60, 2.50)

0.721

− 2.00 (− 2.77, − 1.24)

2.77E-07

0.327

OpenSea

ANKRD28

Body

chr4

cg06690548

139,162,808

− 1.80 (− 2.40, − 1.20)

− 4.25 (− 6.83, − 1.66)

0.002

− 1.93 (− 2.51, − 1.34)

8.51E-11

0.067

OpenSea

SLC7A11

Body

chr5

cg26403843

158,634,085

1.70 (1.06, 2.34)

1.03 (− 0.76, 2.81)

0.257

1.62 (1.02, 2.22)

1.34E-07

0.482

N Shelf

RNF145

Body

chr6

cg13123009

31,681,882

3.34 (2.16, 4.52)

2.74 (− 0.30, 5.79)

0.077

3.26 (2.16, 4.36)

6.17E-09

0.718

OpenSea

LY6G6E

TSS200

chr6

cg17501210

166,970,252

− 1.86 (-2.49, − 1.23)

− 5.21 (− 8.07, -2.36)

0.0005

− 2.02 (− 2.64, − 1.41)

1.18E-10

0.023

OpenSea

RPS6KA2

Body

chr7

cg01676795**

75,586,348

1.92 (1.19, 2.65)

0.96 (− 2.66, 4.59)

0.599

1.88 (1.16, 2.60)

2.59E-07

0.608

OpenSea

POR

Body

chr7

cg19390658*

30,636,176

− 1.53 (-2.07, − 1.00)

− 1.29 (− 3.04, 0.46)

0.146

− 1.51 (− 2.02, − 1.00)

6.86E-09

0.792

S Shore

GARS

Body

chr7

cg21429551*

30,635,762

− 1.28 (− 1.76, -0.80)

− 1.43 (− 2.94, 0.09)

0.065

− 1.29 (− 1.75, − 0.84)

2.29E-08

0.855

S Shore

GARS

Body

chr8

cg20907614**

29,914,963

− 1.97 (-2.72, − 1.22)

− 0.73 (− 3.53, 2.06)

0.602

− 1.88 (− 2.60, -1.16)

3.35E-07

0.397

OpenSea

 

Intergenic

chr10

cg01391548**

97,068,696

− 2.18 (− 2.99, − 1.37)

− 2.73 (− 4.79, − 0.67)

0.010

− 2.25 (− 3.01, − 1.50)

4.43E-09

0.623

OpenSea

 

Intergenic

chr10

cg02556345

124,181,965

− 2.78 (-3.83, − 1.72)

− 2.20 (− 5.91, 1.50)

0.241

− 2.73 (− 3.74, -1.72)

1.22E-07

0.767

OpenSea

PLEKHA1

Body

chr10

cg08284263**

92,958,627

− 3.57 (− 4.90, − 2.24)

− 1.77 (− 5.73, 2.19)

0.376

− 3.38 (− 4.64, − 2.12)

1.46E-07

0.392

OpenSea

 

Intergenic

chr10

cg08994060

6,214,026

− 2.02 (− 2.78, − 1.27)

− 3.25 (− 6.05, − 0.46)

0.023

− 2.11 (− 2.83, − 1.38)

1.35E-08

0.398

OpenSea

PFKFB3

Body

chr10

cg26262157

6,214,079

− 2.13 (− 2.92, − 1.34)

− 3.45 (− 6.11, − 0.79)

0.012

− 2.24 (− 2.99, − 1.48)

5.89E-09

0.344

OpenSea

PFKFB3

Body

chr11

cg00574958

68,607,622

− 9.68 (− 11.83, − 7.53)

− 8.83 (− 13.70, − 3.96)

0.001

− 9.54 (− 11.50, − 7.58)

1.65E− 21

0.751

N Shore

CPT1A

5'UTR

chr11

cg17058475

68,607,737

− 4.52 (− 6.06, − 2.98)

− 5.53 (− 9.14, − 1.91)

0.003

− 4.67 (− 6.09, − 3.26)

8.84E− 11

0.610

N Shore

CPT1A

5'UTR

chr13

cg19750657

38,935,967

2.62 (1.84, 3.40)

2.32 (-1.02, 5.67)

0.171

2.60 (1.85, 3.36)

1.71E-11

0.863

OpenSea

UFM1

3'UTR

chr15

Cg06192883**

52,554,171

3.39 (2.41, 4.37)

3.94 (1.08, 6.80)

0.008

3.45 (2.53, 4.37)

2.31E-13

0.718

OpenSea

MYO5C

Body

chr16

cg26663590

28,959,310

2.27 (1.44, 3.09)

3.59 (0.24, 6.95)

0.036

2.35 (1.55, 3.15)

9.35E-09

0.446

S Shore

 

Intergenic

chr17

cg13274938

38,493,822

3.22 (2.07, 4.36)

3.78 (-0.85, 8.41)

0.109

3.25 (2.14, 4.36)

9.39E-09

0.815

N Shelf

RARA

Body

chr17

cg18772573

71,257,980

2.64 (1.63, 3.65)

3.13 (-1.69, 7.95)

0.201

2.66 (1.67, 3.65)

1.35E-07

0.845

OpenSea

CPSF4L

1stExon

chr17

cg24366564**

2,843,149

2.84 (1.74, 3.93)

-0.91 (-4.26, 2.44)

0.589

2.47 (1.43, 3.50)

3.26E-06

0.035

OpenSea

RAP1GAP2

Body

chr21

cg06500161**

43,656,587

3.75 (2.86, 4.65)

7.01 (3.66, 10.36)

 < 0.001

3.97 (3.11, 4.83)

1.32E-19

0.062

S Shore

ABCG1

Body

chr21

cg08309687£

35,320,596

-2.10 (-2.70, -1.49)

-3.34 (-6.17, -0.51)

0.021

-2.15 (-2.74, -1.56)

7.59E-13

0.392

OpenSea

 

Intergenic

chr21

cg27243685**

43,642,366

3.71 (2.45, 4.97)

10.83 (4.64, 17.02)

0.001

4.00 (2.77, 5.24)

2.13E-10

0.025

S Shelf

ABCG1

Body

chr22

cg09349128

50,327,986

-3.15 (-4.30, -2.01)

-3.71 (-6.95, -0.46)

0.026

-3.22 (-4.30, -2.14)

5.31E-09

0.749

N Shore

 

Intergenic

  1. Chr chromosome, CI Confidence interval, CpG CpG dinucleotide, Effect Effect size; HOMA-IR, homeostatic model assessment–insulin resistance; TSS200, 0–200 bp upstream of transcription start site; TSS1500, 200–1500 bp upstream of transcription start site; UTR, untranslated region. Numbers in bold face are statistically significant
  2. § Annotation used R v.0.6.0.IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450 k methylation arrays
  3. † Each effect size of the CpGs in the discovery stage was at the epigenome-wide significance level (p < 1E-007)
  4. a Effect size adjusted by age and leukocyte heterogeneities (CD8+CD28−CD45RA− T cell, naïve CD8 T cell, plasma blast, CD4+ T cell, natural killer cell, monocyte, and granulocyte)
  5. ¥ p value for Cochran’s Q
  6. * Promoter associated
  7. ** Enhancer associated
  8. £ Enhancer and promoter associated