Table 2.
Top 10 significant smoking-associated DMPs of BS methyl (5mC + 5hmC), true 5mC (oxBS), and 5hmC in MS patients (MS-S vs. MS-NS).
| Probe | P value | Adj. P value | Chr | Position | Gene | Δβ | Island_Rel | Feature | Enhancer |
|---|---|---|---|---|---|---|---|---|---|
| BS | |||||||||
| cg12703333 | 1.1E−10 | 4.3E–05 | chr10 | 76962548 | 0.30 | OpenSea | IGR | ||
| cg09020840 | 1.2E−10 | 4.3E–05 | chr17 | 73087391 | SLC16A5 | 0.21 | S_Shelf | 5ʹUTR | |
| cg22145459 | 4.3E−10 | 1.0E–04 | chr6 | 31693656 | C6orf25 | −0.26 | S_Shore | 3ʹUTR | |
| cg11823253 | 5.7E−10 | 1.0E–04 | chr1 | 213154553 | VASH2 | 0.15 | OpenSea | Body | |
| cg01034754 | 2.1E−09 | 2.6E–04 | chr10 | 30720817 | 0.22 | N_Shore | IGR | ||
| cg06275684 | 2.3E–09 | 2.6E–04 | chr12 | 65074198 | RASSF3 | 0.24 | OpenSea | Body | * |
| cg24439401 | 2.4E–09 | 2.6E–04 | chr3 | 16282260 | 0.15 | OpenSea | IGR | ||
| cg26744946 | 4.6E–09 | 3.9E–04 | chr8 | 145065833 | GRINA | 0.16 | S_Shore | Body | |
| cg11650372 | 4.7E–09 | 3.9E–04 | chr21 | 35171932 | ITSN1 | 0.29 | OpenSea | Body | |
| cg07249224 | 6.0E–09 | 3.9E–04 | chr16 | 30101680 | TBX6 | 0.25 | N_Shore | Body | |
| 5mC | |||||||||
| cg10655682 | 1.6E–08 | 5.8E–03 | chr19 | 4567177 | −0.34 | S_Shore | IGR | * | |
| cg24699021 | 2.2E–08 | 5.8E–03 | chr5 | 172305986 | ERGIC1 | −0.41 | OpenSea | Body | |
| cg22145459 | 3.2E–08 | 5.8E–03 | chr6 | 31693656 | C6orf25 | −0.26 | S_Shore | 3ʹUTR | |
| cg20472746 | 3.7E–08 | 5.8E–03 | chr13 | 42039334 | C13orf15 | −0.19 | OpenSea | Body | |
| cg14223856 | 4.0E–08 | 5.8E–03 | chr9 | 139508740 | −0.35 | OpenSea | IGR | ||
| cg07457727 | 6.6E–08 | 8.0E–03 | chr8 | 131451983 | −0.29 | N_Shelf | IGR | ||
| cg01668352 | 8.6E–08 | 8.0E–03 | chr12 | 64482597 | SRGAP1 | −0.23 | OpenSea | Body | |
| cg24790419 | 8.8E–08 | 8.0E–03 | chr19 | 18385930 | KIAA1683 | −0.24 | OpenSea | TSS1500 | |
| cg01233673 | 1.2E–07 | 9.5E–03 | chr18 | 33517119 | 0.19 | OpenSea | IGR | ||
| cg25468274 | 1.3E–07 | 9.5E–03 | chr1 | 31280338 | −0.22 | Island | IGR | ||
| 5hmC | |||||||||
| cg18513023 | 6.1E–08 | 2.9E–02 | chr6 | 44009266 | 0.13 | OpenSea | IGR | * | |
| cg13297582 | 1.0E–07 | 2.9E–02 | chr18 | 13288627 | LDLRAD4 | 0.08 | OpenSea | 5ʹUTR | |
| cg19800026 | 1.5E–07 | 2.9E–02 | chr5 | 14492945 | TRIO | 0.21 | OpenSea | Body | |
| cg22944934 | 1.6E–07 | 2.9E–02 | chr6 | 31621765 | BAT3 | 0.17 | S_Shore | TSS1500 | |
| cg14341968 | 9.6E–07 | 1.4E–01 | chr9 | 136075868 | 0.04 | S_Shore | IGR | ||
| cg26650480 | 1.2E–06 | 1.4E–01 | chr20 | 4796176 | RASSF2 | 0.11 | OpenSea | 5ʹUTR | |
| cg09655482 | 1.3E–06 | 1.4E–01 | chr10 | 27131072 | ABI1 | 0.11 | OpenSea | Body | |
| cg03964696 | 1.6E–06 | 1.5E–01 | chr2 | 74734085 | PCGF1 | 0.21 | N_Shore | Body | |
| cg22502837 | 2.2E–06 | 1.8E–01 | chr12 | 56137111 | GDF11 | 0.03 | Island | 1stExon | |
| cg19629631 | 4.3E–06 | 3.1E–01 | chr7 | 2060116 | MAD1 L1 | 0.12 | Island | Body | * |
DMPs: differentially methylated positions; BS: bisulfate; MS: multiple sclerosis; S: smoker; NS: non-smoker; IGR: intergenic region; Probe: Illumina probe ID; Adj. P value: Benjamini–Hochberg corrected P value (FDR); Chr: chromosome; Gene: UCSC gene name; Δβ: difference in mean β-values between smokers and non-smokers; Island_Rel: relation to CpG Island; Feature: gene feature; Enhancer: identified enhancer in FANTOM5 consortium; *annotated as enhancer.