Table 1. Top Developmental DMRs which intersect with open chromatin regions in developing knee cartilage.

The largest identified dDMRs (N CpGs>16) which became either hypermethylated (upper) or hypomethylated (lower) across the captured developmental window. The nearest physical gene to each dDMR is listed.

Top hypermethylated DMRs
DMR ID (Cluster)	Chr	Start	End	Gene	Classification/Function	FDR	CpGs (N)
1413 (3)	2	66665027	66668012	MEIS1	Transcriptional regulator of proximodistal limb identity	2.03×10−36	18
1576 (3)	2	119607192	119611880	EN1	Engrailed Homeobox Transcription Factor	2.26×10−44	19
1755 (3)	2	177021702	177030228	HOXD3	Homeobox Transcription Factor	6.31×10−127	39
3054 (3)	5	3597311	3602413	IRX1	Iroquois Homeobox Transcription Factor	1.98×10−18	18
3759 (3)	6	30848726	30851086	DDR1	Discoidin Domain Receptor	2.01×10−97	18
3825 (3)	6	32115979	32118204	PRRT1	Transmembrane Protein	1.43×10−69	21
4430 (3)	7	27142100	27143788	HOXA2	Homeobox Transcription Factor	2.76×10−22	20
4444 (3)	7	27181067	27189610	HOXA3	Homeobox Transcription Factor	1.48×10−140	59
6992 (3)	12	16760056	16763480	MGST1	Glutathione S-Transferase	1.49×10−104	19
8319 (3)	15	74423308	74427499	ISLR2	Immunoglobulin Superfamily	8.15×10−76	19
9322 (3)	17	48911141	48913317	WFIKKN2	Serine and metalloprotease inhibitor	8.44×10−260	22
10141 (3)	20	36145902	36148775	BLCAP	Regulates cell proliferation and apoptosis	1.86×10−112	24
10351 (3)	21	38076709	38082613	SIM2	Basic helix-loop-helix transcription factor	7.42×10−37	21
Top hypomethylated DMRs
DMR ID (Cluster)	Chr	Start	End	Gene	Classification/Function	FDR	CpGs (N)
2153 (2)	3	46447254	46449636	CCRL2	Chemokine receptor	3.11×10−127	17
2624 (2)	4	1202780	1206150	SPON2	ECM Glycoprotein	3.11×10−105	17
3804 (2)	6	32014059	32016535	TNXB	ECM Glycoprotein	3.80×10−117	34
3813 (2)	6	32048632	32050947	TNXB	ECM Glycoprotein	1.04×10−67	19