Table 2 Discovery epigenome-wide association analysis of height in childhood in the MMNP cohort

From: DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood

CpG ID

n

Effect sizea

95% CI

P value

FDR

Chr

CpG position (hg19)

Gene nameb

cg11047325

685

0.21

0.14, 0.28

3.0E−11

2.4E-05

chr17

76,354,934

SOCS3

cg13343932

685

0.25

0.18, 0.31

5.8E-11

4.6E-05

chr17

76,355,061

SOCS3;LOC101928674

cg18181703

685

0.30

0.24, 0.37

3.0E-10

2.4E-04

chr17

76,354,621

SOCS3

cg09383132

684

0.37

0.32, 0.42

2.3E-07

1.9E-01

chr19

45,258,265

BCL3

cg09050300

685

−0.26

−0.21, −.31

4.0E-07

3.2E-01

chr5

95,511,892

LOC101929710

cg19723657

685

0.15

0.10, 0.20

5.4E-07

4.4E-01

chr13

92,002,951

MIR17HG;MIR20A;MIR19B1; MIR92A1;MIR18A;MIR19A

cg24629020

685

-0.14

−0.09, −0.19

6.3E-07

5.1E-01

chr12

15,752,531

Intergenic

cg12170787

685

0.31

0.26, 0.36

1.5E-06

1.0E + 00

chr19

1,130,965

SBNO2

cg14972576

685

0.21

0.16, 0.25

2.8E-06

1.0E + 00

chr5

97,645,526

Intergenic

cg14472390

685

−0.14

−0.09, −0.18

2.9E-06

1.0E + 00

chr5

140,740,387

PCDHGA4;PCDHGA2;PCDHGB2; PCDHGA1;PCDHGA3

  1. MMNP Mumbai Maternal Nutrition Project, CI confidence interval, FDR false discovery rate, Chr chromosome, n sample size, CpG ID CpG probe on the Illumina Infinium methylation EPIC Beadchip array.
  2. EWAS analysis was conducted using multiple linear regression models with a predefined FDR threshold of 0.05. The Benjamini–Hochberg method was used for multiple testing correction.
  3. aEffect size indicates the change in height in centimetres associated with a 1% change in CpG methylation. The top three hits pass the FDR < 5% threshold for significance.
  4. bUCSC reference gene name from EPIC manifest file. P value: statistical significance.
  5. The top ten CpGs ranked by P value are shown.
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