Table 2.

Median DNA methylation levels by global features across tissues

	# CpGs (Blood/Brain)	T1	T2	Brain	p Δ
Island features
Island	135,303/135,303	0.059	0.060	0.058	<0001
North shore	55,328/55,328	0.481	0.485	0.442	<0001
South shore	43,325/43,325	0.466	0.471	0.415	<0001
North shelf	20,732/20,732	0.845	0.846	0.826	<0001
South shelf	18,409/18,409	0.847	0.848	0.830	<0001
Gene features
TSS1500	60,703/60,703	0.172	0.176	0.161	<0001
TSS200	47,242/47,242	0.048	0.049	0.048	.031
5’UTR	37,987/37,987	0.141	0.144	0.135	<0001
1stExon	20,239/20,239	0.062	0.063	0.059	.002
Gene body	141,917/141,917	0.817	0.819	0.755	<0001
3’UTR	15,188/15,188	0.853	0.853	0.815	<0001
Chromatin structure*
1_TssA	60,614/125,965	0.039	0.040	0.048	<0001
2_TssAFlnk	41,806/21,400	0.093	0.095	0.187	<0001
3_TxFlnk	29,974/872	0.037	0.038	0.497	<0001
4_Tx	28,060/23,942	0.895	0.895	0.863	<0001
5_TxWk	33,593/55,988	0.876	0.877	0.835	<0001
6_EnhG	4,486/4399	0.856	0.858	0.701	<0001
7_Enh	23,797/24,161	0.741	0.746	0.586	<0001
8_ZNF/Rpts	894/702	0.852	0.851	0.673	<0001
9_Het	2,119/1,528	0.805	0.805	0.806	0.775
10_TssBiv	3,872/12,473	0.064	0.066	0.087	<0001
11_BivFlnk	9,281/4,212	0.090	0.094	0.091	0.008
12_EnhBiv	9,381/3,645	0.146	0.151	0.186	<0001
13_ReprPC	15,708/17,536	0.254	0.263	0.264	<0001
14_ReprPCWk	39,455/36,929	0.684	0.683	0.804	<0001
15_Quies	117,092/86,380	0.841	0.841	0.848	<0001

^*1: Active TSS; 2: Flanking Active TSS; 3: Transcription at gene 5’ and 3’; 4: Strong transcription; 5: Weak transcription; 6: Genic enhancers; 7: Enhancers; 8: ZNF genes & repeats; 9: Heterochromatin; 10: Bivalent/Poised TSS; 11: Flanking Bivalent TSS/Enh: 12: Bivalent Enhancer; 13: Repressed PolyComb; 14: Weak Repressed PolyComb; 15: Quiescent/Low. Detailed description is reported previously [17].

^ΔEach p-value was derived from a non-parametric Kruskal-Wallis test which compares the difference of median methylation levels between T1, T2 and brain.