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

Table 4 Characterization of DMRs identified after cell type correction

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	Yes^a
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

“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

ISSN: 1756-994X