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Table 1 Genome-wide scan of DNA methylation for an association with fasting glucose concentrations (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†a (95% CI)

Effect a (95% CI)

p

Effect (95% CI)

p

pQÂ¥

chr1

cg14476101

120,255,992

 − 0.50 (− 0.66, − 0.35)

 − 1.08 (− 1.79, − 0.38)

0.003

 − 0.53 (− 0.68, − 0.38)

4.37E − 12

0.111

S Shore

PHGDH

Body

chr1

cg19693031

145,441,552

 − 1.11 (− 1.30, − 0.93)

 − 1.93 (− 2.55, − 1.30)

 < 0.0026

 − 1.18 (− 1.36, − 1.00)

1.10E − 38

0.013

OpenSea

TXNIP

3'UTR

chr2

cg00765233*

235,877,260

 − 1.11 (− 1.49, − 0.74)

 − 2.70 (− 5.67, 0.28)

0.075

 − 1.14 (− 1.51, − 0.77)

1.92E − 09

0.294

OpenSea

SH3BP4

5'UTR

chr4

cg06690548

139,162,808

 − 0.50 (− 0.70, − 0.31)

 − 0.74 (− 1.70, 0.23)

0.132

 − 0.51 (− 0.70, − 0.32)

9.65E − 08

0.638

OpenSea

SLC7A11

Body

chr8

cg00345025

743,875

 − 0.79 (− 1.09, − 0.49)

 − 0.46 (− 1.65, 0.73)

0.444

 − 0.77 (− 1.06, − 0.48)

2.35E − 07

0.594

N Shore

 

Intergenic

chr9

cg14148209*

7,543,165

 − 1.65 (− 2.16, − 1.13)

 − 0.25 (− 3.52, 3.01)

0.877

 − 1.61 (− 2.12, − 1.11)

3.93E − 10

0.402

OpenSea

 

Intergenic

chr10

cg01391548*

97,068,696

 − 0.70 (− 0.96, − 0.44)

 − 0.53 (− 1.28, 0.23)

0.167

 − 0.68 (− 0.92, − 0.43)

6.21E − 08

0.675

OpenSea

 

Intergenic

chr10

cg02556345

124,181,965

 − 0.88 (− 1.22, − 0.54)

 − 0.57 (− 1.89, 0.76)

0.398

 − 0.86 (− 1.19, − 0.53)

2.60E − 07

0.648

OpenSea

PLEKHA1

Body

chr10

cg08994060

6,214,026

 − 0.64 (− 0.88, − 0.39)

 − 0.69 (− 1.71, 0.32)

0.179

 − 0.64 (− 0.87, − 0.40)

1.02E − 07

0.915

OpenSea

PFKFB3

Body

chr10

cg26262157

6,214,079

 − 0.68 (− 0.94, − 0.43)

 − 0.89 (− 1.85, 0.08)

0.070

 − 0.70 (− 0.94, − 0.45)

2.09E − 08

0.685

OpenSea

PFKFB3

Body

chr11

cg00574958

68,607,622

 − 2.92 (− 3.62, − 2.23)

 − 2.26 (− 4.05, − 0.46)

0.014

 − 2.83 (− 3.48, − 2.19)

7.60E − 18

0.494

N Shore

CPT1A

5'UTR

chr11

cg11588197

128,391,494

 − 0.74 (− 1.02, − 0.47)

0.33 (− 0.56, 1.22)

0.462

 − 0.65 (− 0.91, − 0.38)

1.34E − 06

0.022

N Shore

ETS1

Body

chr11

cg17058475

68,607,737

 − 1.44 (− 1.94, − 0.95)

 − 1.30 (− 2.63, 0.02)

0.054

 − 1.42 (− 1.89, − 0.96)

1.48E − 09

0.845

N Shore

CPT1A

5'UTR

chr12

cg10877979

131,569,407

 − 1.31 (− 1.77, − 0.85)

 − 0.52 (− 3.81, 2.76)

0.753

 − 1.29 (− 1.75, − 0.84)

3.03E − 08

0.637

N Shelf

GPR133

Body

chr13

cg19750657

38,935,967

0.69 (0.44, 0.94)

0.04 (− 1.17, 1.24)

0.951

0.66 (0.41, 0.91)

1.53E − 07

0.293

OpenSea

UFM1

3'UTR

chr20

cg00872151

59,964,387

 − 2.36 (− 3.23, − 1.48)

 − 0.80 (− 4.86, 3.26)

0.697

 − 2.29 (− 3.14, − 1.43)

1.62E − 07

0.456

N Shore

CDH4

Body

chr21

cg06500161*

43,656,587

0.83 (0.53, 1.12)

1.69 (0.43, 2.94)

0.009

0.87 (0.59, 1.15)

1.68E − 09

0.184

S Shore

ABCG1

Body

chr21

cg08309687**

35,320,596

 − 0.52 (− 0.71, − 0.32)

 − 1.11 (− 2.12, − 0.10)

0.032

 − 0.54 (− 0.73, − 0.35)

3.42E − 08

0.254

OpenSea

 

Intergenic

chr21

cg17648210

46,352,817

1.41 (0.88, 1.93)

1.14 (− 2.45, 4.73)

0.530

1.40 (0.88, 1.92)

1.16E − 07

0.883

Island

 

Intergenic

  1. Chr Chromosome, CI Confidence interval, CpG CpG dinucleotide, Effect Effect size; 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. * Enhancer associated
  7. ** Enhancer and promoter associated