Table 4.
Influence of genetic variants near the replicated DMRs in ALSPAC
| ACE | DMR | Nr CpGs | Gene | Original analysis (Directiona, p-value) | Nr SNPs (within 1MB, associated one CpG (p < 0.05)) | Sample size | Sensitivity analysis, including SNPs (Directiona, p-value)b |
|---|---|---|---|---|---|---|---|
| ACE count score | chr8: 145654565-145654855 | 5 | VPS28, TONSL | ----- p = 7.5e−08* |
8 | 618 | ----- p = 0.0020 |
| Parent mentally ill | chr12: 14720726-14721289 | 10 | PLBD1 | -++-++++++ p = 0.0058 |
28 | 532 | --+±++++++ p = 0.0496 |
| Parent mentally ill | chr1: 3104999-3105327 | 5 | PRDM16 | ----- p = 0.001 |
16 | 672 | ----- p = 0.001 |
| Parent physically ill | chr15: 81426347-81426670 | 9 | C15orf26 | +++++++++p = 0.011 | 20 | 609 | +++++++++p = 0.0010 |
| Parent physically ill | chr22: 27834439-27834630 | 3 | n/a | --- p = 6.9e−06* |
35 | 686 | --- p = 1.207e−05* |
| Parent physically ill | chr8: 144120335-144120707 | 7 | C8orf31 | +++++++ p = 4.4e−06* |
13 | 673 | +++++++ p = 7.998e−05* |
| Parent died | chr15: 40364524-40364863 | 3 | n/a | +++ p = 6.3e−07* |
19 | 605 | +++ p = 8.915e−06* |
| Parent died | chr7: 24323261-24323940 | 9 | NPY | +++++++++ p = 9.2e−07* |
40 | 584 | +++++-+++ p = 0.0005 |
| Parent died | chr2: 18766018-18766295 | 4 | NT5C1B | --- + p = 9.8e−06* | 27 | 520 | -± -- p = 0.0289 |
aDirection of effect for each individual CpG that is part of the DMR was derived from the regression coefficients for individual CpGs
bThe CpGs with a different direction of effect in the sensitivity analysis are underlined and in red.
*DMR passed Šidák correction for multiple testing in comb-p