Table 2.
Forty-eight differentially methylated CpG sites in OMD vs OMND with epigenome-wide significance
| CpG | CpG position | Gene/CpG island | Position in gene | Effect, % | 95% CI | Association p value | FDR p value |
|---|---|---|---|---|---|---|---|
| cg21192468 | chr9:139092501 | LHX3 | Body | 4.5 | 3.1, 5.9 | 8.3 × 10−10 | 1.0 × 10−4 |
| cg14381623a | chr9:139091650 | LHX3 | Body | 3.3 | 2.2, 4.5 | 1.5 × 10−8 | 2.0 × 10−4 |
| cg15796459 | chrX:9858910 | SHROOM2 | Body | −1.6 | −2.2, −1.1 | 5.7 × 10−8 | 6.7 × 10−4 |
| cg20749955 | chr8:9009401 | PPP1R3B | TSS1500 | −3.7 | −5.2, −2.3 | 1.3 × 10−7 | 1.2 × 10−3 |
| cg12140144 | chr1:2984275 | PRDM16 | TSS1500 | 1.1 | 0.5, 1.6 | 5.6 × 10−7 | 5.4 × 10−3 |
| cg06717221 | chr19:1790921 | ATP8B3 | Body | −3.0 | −4.1, −1.8 | 1.3 × 10−6 | 8.5 × 10−3 |
| cg15833797a | chr9:139091875 | LHX3 | Body | 2.3 | 1.4, 3.2 | 1.6 × 10−6 | 9.3 × 10−3 |
| cg14605520a | chr9:139094350 | LHX3 | Body | 3.2 | 1.8, 4.6 | 1.8 × 10−6 | 1.0 × 10−2 |
| cg10772621 | chr19:54410999 | chr19:54411376–54411968 | - | −1.8 | −2.5, −1.0 | 2.1 × 10−6 | 1.0 × 10−2 |
| cg25952247a | chr9:139092873 | LHX3 | Body | 2.8 | 1.7, 4.0 | 2.1 × 10−6 | 9.3 × 10−3 |
| cg20345234 | chr10:65801377 | chr10:65800729–65801528 | - | −2.3 | −3.2, −1.4 | 3.4 × 10−6 | 1.5 × 10−2 |
| cg00762450 | chr9:69381140 | ANKRD20A4 | TSS1500 | 1.4 | 0.8, 1.9 | 4.1 × 10−6 | 1.7 × 10−2 |
| cg13700073 | chr17:79495324 | FSCN2 | TSS200 | −1.6 | −2.3, −0.9 | 4.3 × 10−6 | 1.7 × 10−2 |
| cg20769177 | chr17:44928516 | WNT9B | TSS1500 | 2.7 | 1.6, 3.8 | 4.5 × 10−6 | 1.7 × 10−2 |
| cg08292290 | chr14:96010497 | GLRX5 | 3′ UTR | −0.6 | −0.8, −0.3 | 4.6 × 10−6 | 1.6 × 10−2 |
| cg06268875 | chr18:11147385 | PIEZO2 | Body | 4.6 | 2.7, 6.6 | 5.1 × 10−6 | 1.7 × 10−2 |
| cg04350311 | chr22:37821982 | ELFN2 | 5′ UTR | 1.6 | 0.9, 2.4 | 5.7 × 10−6 | 1.8 × 10−2 |
| cg15183961 | chr9:43134756 | ANKRD20A2 | TSS1500 | 1.6 | 0.9, 2.3 | 5.9 × 10−6 | 1.8 × 10−2 |
| cg26671988 | chr5:102089760 | chr5:102090439–102091241 | - | 2.1 | 1.2, 3.1 | 6.3 × 10−6 | 1.8 × 10−2 |
| cg17186803 | chr11:118023038 | SCN4B | Body | 1.2 | 0.7, 1.8 | 7.3 × 10−6 | 2.1 × 10−2 |
| cg24049468 | chr1:65615281 | AK3 | Body | 2.5 | 1.4, 3.7 | 7.8 × 10−6 | 2.1 × 10−2 |
| cg27222147 | chr12:2224755 | CACNA1C | Body | −0.9 | −1.3, −0.5 | 7.8 × 10−6 | 2.0 × 10−2 |
| cg08370430 | chr17:12927578 | chr17:12927455–12928747 | - | 1.3 | 0.7, 1.9 | 8.0 × 10−6 | 2.0 × 10−2 |
| cg15618978 | chr3:160167990 | TRIM59 | TSS1500 | 1.4 | 0.8, 2.1 | 8.2 × 10−6 | 2.0 × 10−2 |
| cg07464358 | chr7:100952364 | - | - | 0.9 | 0.5, 1.3 | 8.4 × 10−6 | 2.0 × 10−2 |
| cg24996440 | chr2:3583570 | chr2:3583550–3584833 | - | −2.0 | −2.9, −1.1 | 9.0 × 10−6 | 2.0 × 10−2 |
| cg03862414 | chr17:40824241 | PLEKHH3 | Body | 2.2 | 1.2, 3.2 | 9.0 × 10−6 | 2.0 × 10−2 |
| cg05772155a | chr10:65801432 | chr10:65800729–65801528 | - | −3.4 | −5.0, −1.9 | 9.9 × 10−6 | 2.1 × 10−2 |
| cg21172615a | chr9:139092102 | LHX3 | Body | 2.6 | 1.5, 3.8 | 1.1 × 10−5 | 2.4 × 10−2 |
| cg20941258 | chr3:46618668 | TDGF1 | TSS1500 | 2.4 | 1.3, 3.4 | 1.1 × 10−5 | 2.4 × 10−2 |
| cg08414676 | chr15:45314943 | SORD | TSS1500 | −2.4 | −3.5, −1.4 | 1.2 × 10−5 | 2.5 × 10−2 |
| cg00509616 | chr15:57884415 | GCOM1 | Body | 1.2 | 0.6, 1.7 | 1.2 × 10−5 | 2.4 × 10−2 |
| cg09674170 | chr16:3062382 | CLDN9 | TSS200 | 2.9 | 1.6, 4.1 | 1.4 × 10−5 | 2.8 × 10−2 |
| cg07993743a | chr17:44928288 | WNT9B | TSS1500 | 2.1 | 1.1, 3.0 | 1.5 × 10−5 | 2.9 × 10−2 |
| cg04645534 | chr8:23712550 | STC1 | TSS1500 | −2.9 | −4.1, −1.6 | 1.6 × 10−5 | 2.9 × 10−2 |
| cg04413090 | chr16:28302913 | SBK1 | TSS1500 | 1.0 | 0.5, 1.4 | 1.6 × 10−5 | 2.9 × 10−2 |
| cg13427473 | chr15:88406836 | - | - | −0.7 | −1.0, −0.4 | 1.7 × 10−5 | 3.0 × 10−2 |
| cg16426215 | chr16:56706854 | chr16:56709677–56709953 | - | −1.5 | −2.1, −0.8 | 2.0 × 10−5 | 3.6 × 10−2 |
| cg24503407 | chr1:205819492 | PM20D1 | TSS1500 | −3.9 | −6.0, −1.9 | 2.2 × 10−5 | 3.9 × 10−2 |
| cg12875241 | chrX:9734063 | GPR143 | TSS200 | 4.1 | 2.2, 5.9 | 2.2 × 10−5 | 3.8 × 10−2 |
| cg14732789 | chr20:29537189 | chr20:29534910–29535208 | - | −1.4 | −2.1, −0.8 | 2.2 × 10−5 | 3.7 × 10−2 |
| cg14105781 | chrX:9433597 | TBL1X | 5′ UTR | 1.5 | 0.8, 2.2 | 2.4 × 10−5 | 4.1 × 10−2 |
| cg08911291 | chr9:44119413 | chr9:44118137–44120175 | - | 2.4 | 1.3, 3.5 | 2.4 × 10−5 | 4.0 × 10−2 |
| cg05806645a | chr8:9009352 | PPP1R3B | TSS1500 | −2.2 | −3.3, −1.1 | 2.5 × 10−5 | 4.0 × 10−2 |
| cg25629768 | chr19:2428567 | LMNB2 | TSS1500 | 1.4 | 0.7, 2.1 | 2.8 × 10−5 | 4.4 × 10−2 |
| cg16482344 | chr10:42970987 | LINC00839 | Body | −3.6 | −5.2, −1.9 | 2.8 × 10−5 | 4.3 × 10−2 |
| cg25949304 | chr5:140815218 | PCDHGA4 | Body | −2.8 | −4.1, −1.5 | 3.0 × 10−5 | 4.7 × 10−2 |
| cg27073142a | chr15:45314933 | SORD | TSS1500 | 4.3 | 2.3, 6.2 | 3.3 × 10−5 | 5.0 × 10−2 |
CpG position is given in a chromosome:base pair format
A CpG is assigned to a gene if it is located within the gene region; if it is not within a gene region, the start/stop of the CpG island is given
TSS1500, CpG is 1500 base pairs away from the TSS and located in the 5′ flanking region of the TSS; TSS200, CpG is 200 base pairs away from the TSS and located in the 5′ flanking region of the TSS
Effect sizes are shown for the model with Beta-value as the dependent variable, while p values are reported for the model with M-value as the dependent variable
The effect represents the difference in the percentage of DNA methylation in OMD compared with OMND. The 95% CI of this effect is shown in the adjacent column
a
These CpG sites are secondary signals of a differentially methylated gene/region