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Table 3 Top 5mC-DMPs, 5hmC-DhMPs and BS-DMPs (adjusted P value < 0.05) associated with multiple sclerosis (cohort 2).

From: Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis

probeID Ch Pos mean_MS mean_ctr Δβ P value adj. P value Gene namea Featurea Overlap DMP Overlap DMR
5mC-DMP
 cg06077821 5 180048893 0.50 0.58 − 0.08 7.8E−08 6.6E−03 FLT4 Body 5hmC 5mC, 5hmC
 cg04313978 7 158271081 0.60 0.72 − 0.13 6.4E−08 6.6E−03 PTPRN2 Body 5hmC 5mC, 5hmC
 cg24172278 7 1526831 0.67 0.75 − 0.08 1.5E−07 8.4E−03 INTS1 Body 5mC
 cg09226185 7 157342801 0.73 0.81 − 0.08 4.1E−07 9.8E−03 PTPRN2 Body 5hmC 5mC, 5hmC
 cg10738865 11 2356706 0.64 0.75 − 0.11 7.2E−10 3.0E−04 5hmC 5mC, 5hmC
 cg12910900 12 13155162 0.62 0.70 − 0.08 2.3E−07 8.9E−03 HTR7P Body 5hmC 5mC, 5hmC
 cg06703573 16 1364331 0.48 0.58 − 0.10 2.6E−08 5.4E−03 UBE2I Body 5hmC 5mC, 5hmC
 cg20942310 17 73728061 0.69 0.78 − 0.08 1.6E−07 8.4E−03 ITGB4 Body 5hmC 5mC, 5hmC
 cg15659599 19 55098842 0.36 0.43 − 0.07 4.5E−07 9.8E−03 LILRA2 3′UTR 5hmC
 cg25934700 22 50644755 0.52 0.66 − 0.14 2.1E−07 8.7E−03 SELO Body 5hmC 5mC, 5hmC
5hmC-DhMP
 cg18213443 1 4221388 0.21 0.10 0.11 4.7E−07 5.5E−03 5mC 5hmC
 cg27331828 1 196619631 0.27 0.08 0.19 2.9E−07 4.6E−03 CFH TSS1500 5hmC
 cg04639610 2 74942001 0.18 0.03 0.15 1.4E−07 4.6E−03 5hmC
 cg23376467 5 121464241 0.16 0.05 0.11 2.8E−07 4.6E−03 ZNF474 TSS1500
 cg06996555 7 151542415 0.25 0.12 0.13 1.0E−06 8.3E−03 PRKAG2 Body 5mC 5hmC
 cg10738865 11 2356706 0.26 0.15 0.12 1.4E−08 1.5E−03 5mC 5mC, 5hmC
 cg15426626 12 132984261 0.21 0.10 0.11 1.7E−07 4.6E−03 5mC 5hmC
 cg01863290 14 96730669 0.25 0.11 0.13 5.0E−07 5.5E−03 BDKRB1 Body 5mC 5hmC
 cg25594736 15 67391147 0.19 0.09 0.10 9.1E−07 8.3E−03 SMAD3 Body
 cg06703573 16 1364331 0.38 0.28 0.11 1.9E−07 4.6E−03 UBE2I Body 5mC 5mC, 5hmC
BS-DMP
 cg18327319 1 11795409 0.82 0.66 0.17 1.6E−05 2.8E−02 AGTRAP TSS1500 5hmC
 cg16732616 1 50886782 0.09 0.21 − 0.12 4.3E−06 2.2E−02 DMRTA2 Body 5hmC 5hmC, BS
 cg11750112 1 64938742 0.73 0.83 − 0.10 1.4E−05 2.7E−02 CACHD1 Body
 cg18864124 2 227288863 0.71 0.56 0.14 8.9E−06 2.6E−02 5hmC 5hmC
 cg02379784 5 471326 0.62 0.74 − 0.11 1.0E−05 2.6E−02 LOC25845 Body 5hmC, BS
 cg08376583 6 32222492 0.33 0.54 − 0.21 8.6E−06 2.6E−02
 cg25670061 6 163612896 0.77 0.66 0.10 7.2E−06 2.6E−02 PACRG Body
 cg00459997 12 130621721 0.75 0.63 0.12 2.8E−06 2.2E−02 5mC
 cg20165520 13 113637829 0.69 0.57 0.12 1.5E−05 2.7E−02 MCF2L Body BS
 cg05491587 18 77659695 0.59 0.69 − 0.10 6.6E−06 2.5E−02 KCNG2 Body BS
  1. aFrom UCSC annotations. DMP differentially methylated position, DMR differentially methylated region, 5mC oxBS-generated “true” methylation, 5hmC hydroxymethylation, BS bisulfite-generated, Ch Chromosome, Pos position, MS Multiple Sclerosis, ctr non-neurological controls, Δβ delta β-value, adj. P value adjusted P-value, TSS transcription starting site