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Table 4 Characterization of DMRs identified after cell type correction

From: High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

DMR name Gene (distance to TSS) Projection Location: gene Location: CGI EIRA
DMR1 PCDHB14 (+224) 0.02 Promoter Shore No
DMR2 SLCO2B1 (+91266), ARRB1 (+109444) 0.28 Intergenic CGI/Shore Yesa
DMR3 NUDT10 (−3524) 0.48 Gene body - No
DMR4 SAMD4A (−2474) 0.67 Gene body CGI Yes +
DMR5 TCF7L1 (+1479), TGOLN2 (+193161) 0.30 Promoter CGI Yes a +
DMR6 PAPOLA (+44) 0.56 Promoter CGI Yes a +
DMR7 AK3 (−275) 0.84 Promoter CGI Yes +
DMR8 ZNF281 (+326) 0.89 Promoter CGI Yes +
DMR9 NHLH2 (+632) 0.55 Promoter Shore Yes
DMR10 LINGO1 (−186249), TBC1D2B (+259036) 0.45 Intergenic CGI/Shore No
DMR11 SP5 (+412) 0.83 Promoter CGI Yes +
DMR12 PLA2G15 (−592) 0.31 Promoter CGI/Shore Yes +
DMR13 TMCO3 (−346) 0.73 Promoter CGI Yes +
DMR14 LZTR1 (−62745), CRKL (+2099) 0.13 Extended promoter Shore *
DMR15 LRRC37A (−107090), KIAA1267 (−15809) 0.94 Gene body - *
DMR16 CA8 (+2720) 0.91 Extended promoter - *
DMR17 HTR2C (−3412) 0.20 Gene body Shore *
DMR18 EXOSC1 (−4655), ZDHHC16 (+4493) 0.69 Gene body Shore No
  1. “Gene” provides information on the closest genes and the distance to the transcription start site (TSS). “Location: gene” and “Location: CGI” denote the locations of the center of the DMR in relation to a gene or a CpG island. “EIRA” is “yes” if the DMR overlaps with a DMP from the EIRA cohort [2] or if it is alocated within 1000 bp of one; a plus sign in the EIRA column denotes the same direction of change. “Projection” denotes the permuted p value of the DMRs of TS1 and TS2 when using methylation data from TS2 and TS1, respectively (see the “Projection analysis” section in the “Methods”); p values in bold are those <0.05. An asterisk denotes that no probes within 500 bp of the DMR are available in the Illumina 450 K array and no comparison is thus possible