Genome-wide DNA methylation study of hip and knee cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis

Table 2 Top CpG sites differentially methylated in knee/hip OA compared to OA-free cartilage^a

CpG	Δβ	P-value	Gene symbol	UCSC location group	UCSC island group	Enhancer
cg22669656	−0.22	0.0004	PGS1	Body		Yes
cg11905061	0.21	0.0004	AGAP1	Body	S_Shore
cg27390206	−0.21	0.0002	BLMH	Body		Yes
cg09140531	−0.21	0.0004				Yes
cg14223856	−0.21	0.0005				Yes
cg13688786	−0.20	0.0003	MYO18A	Body		Yes
cg22022821	−0.20	0.0002
cg10340048	−0.20	0.0002				Yes
cg02464866	−0.20	0.0004			N_Shore	Yes
cg05033952	−0.20	0.0001			N_Shore
cg19629120	−0.19	0.0005	EFCAB6	3'UTR
cg04973183	−0.19	0.0004				Yes
cg00150785	−0.19	0.0004			N_Shore	Yes
cg12027254	−0.19	0.00004	TNRC6C	Body		Yes
cg14068309	−0.19	0.0002	EIF2B1	3'UTR
cg13556934	−0.18	0.0003			N_Shelf	Yes
cg14022778	−0.18	0.0004	FHAD1	Body
cg02017450	0.18	0.0004				Yes
cg23074762	−0.18	0.0002	CHSY1	Body		Yes
cg04228742	−0.18	0.0002
cg22203890	−0.18	0.0005
cg17611936	0.18	0.0003	PRKAG2	Body
cg07107113	−0.17	0.0004	FBLIM1	5'UTR	S_Shore
cg12582728	−0.17	0.0004				Yes
cg07404223	−0.17	0.0002				Yes
cg25002179	−0.16	0.0005	STARD13	5'UTR;Body;TSS1500		Yes
cg17025149	−0.16	0.0001				Yes
cg26043955	−0.16	0.0004				Yes
cg26919145	−0.16	0.0002	LDLRAD3	Body		Yes
cg09425279	−0.16	0.0003			N_Shelf
cg06712559	0.16	0.0004	AGRN	Body	Island	Yes
cg02099390	−0.16	0.0002	OSBPL10	Body		Yes
cg11805414	−0.16	0.0005				Yes
cg04038680	−0.16	0.0002	SHISA9	Body		Yes
cg25341923	−0.15	0.0001	KRTAP4-7	TSS1500
cg14728071	−0.15	0.00004	MLLT10	3'UTR
cg03667871	−0.15	0.0004	NEK7	TSS1500	N_Shore
cg13258453	−0.15	0.0002				Yes
cg23010507	−0.15	0.0001			S_Shelf	Yes
cg12158488	−0.15	0.0002				Yes

^aΔβ: difference in methylation value between sample groups (OA cartilage - intact); UCSC: University of California, Santa Cruz; 5’-UTR: 5’-untranslated region; N: North; S: South; TSS 200: within 200 bp of transcription start site

ISSN: 1471-2474