Table 2.
Discovery epigenome-wide association analysis of height in childhood in the MMNP cohort
| 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 |
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.
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.
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.
bUCSC reference gene name from EPIC manifest file. P value: statistical significance.
The top ten CpGs ranked by P value are shown.