Order	SeqName	SeqType	IsAE	Lum_Epi	Lum_Epi2	Myo_Epi	Myo_Epi2	hESCs	StemLike	vHMECs
1	ZNF688	Gene	0	16.80	11.78	15.61	10.78	20.30	10.15	13.41
2	395216	Transcript	0	15.55	6.06	11.45	5.63	33.39	3.68	6.75
3	321694	Transcript	0	1.17	0.00	0.09	0.50	6.55	0.97	0.00
4	395222	Transcript	0	1.50	1.43	2.01	0.45	0.92	0.92	1.19
5	395219	Transcript	0	8.25	4.06	7.41	7.57	1.63	8.05	3.83
6	223459	Transcript	0	1.54	0.00	0.11	1.03	0.24	0.00	2.73
7	IG36	Intergenic	0	5.50	8.36	4.19	4.13	16.61	7.73	4.49
8	IG36_AR3	ActiveIntergenicRegion	0	23.69	37.93	18.14	18.17	63.24	36.73	19.78
9	IG36_SR1	SilentIntergenicRegion	0	2.47	1.52	1.19	0.83	12.25	1.33	1.15
10	ER1a	ExonRegion	0	2.57	2.29	0.00	0.51	9.32	4.11	1.58
11	E1_Ab	KnownBoundary	0	4.14	3.05	1.52	1.68	10.26	6.94	2.21
12	ER1b	ExonRegion	1	8.35	9.12	6.30	3.73	9.63	13.94	5.00
13	E1_Da	KnownBoundary	0	2.07	0.00	0.00	1.22	6.18	0.00	0.00
14	E1a_E2a	KnownJunction	1	6.26	17.86	11.63	8.13	14.43	11.93	4.47
15	ER1c	ExonRegion	0	1.56	0.78	0.02	0.45	2.08	0.03	0.00
16	E1b_E2a	KnownJunction	0	0.00	1.44	1.70	0.00	0.00	0.00	0.00
17	ER2a	ExonRegion	0	19.77	26.58	25.12	18.09	25.20	25.51	13.99
18	E2a_E3a	KnownJunction	1	18.11	29.29	41.26	21.32	20.59	38.99	20.41
19	ER3a	ExonRegion	0	19.21	26.62	22.79	20.27	26.84	17.28	19.64
20	E3_Da	KnownBoundary	1	17.77	14.13	36.85	17.26	29.92	12.84	19.05
21	E3a_E4b	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
22	ER3b	ExonRegion	0	22.43	10.23	24.11	13.95	31.75	8.31	15.93
23	E3_Db	KnownBoundary	0	2.09	1.05	6.71	2.82	5.92	0.00	2.57
24	ER3c	ExonRegion	0	15.55	6.06	11.45	5.63	33.39	3.68	6.75
25	E3_Dc	NovelBoundary	0	68.04	51.94	48.89	30.07	30.59	30.18	24.31
26	I3	Intron	0	8.52	3.45	8.29	3.02	7.65	2.39	4.07
27	I3_AR1	ActiveIntronRegion	0	16.45	4.52	16.10	4.64	21.76	4.87	5.18
28	I3_AR2	ActiveIntronRegion	0	2.71	2.04	2.89	0.77	8.69	1.73	1.20
29	I3_AR3	ActiveIntronRegion	0	9.94	4.37	9.72	3.72	4.70	2.33	5.20
30	E4_Aa	NovelBoundary	0	15.84	14.55	20.88	10.02	1.18	9.09	7.08
31	ER4a	ExonRegion	0	12.24	5.86	12.91	7.28	3.26	13.22	7.09
32	E4_Ab	KnownBoundary	0	9.36	5.44	15.42	9.62	2.19	8.04	6.08
33	ER4b	ExonRegion	0	7.86	5.60	7.46	6.33	2.24	6.89	5.02
34	E4_Da	KnownBoundary	0	6.28	1.63	9.00	2.30	3.32	0.00	9.46
35	E4a_E6a	KnownJunction	0	4.26	2.26	1.91	7.86	0.00	2.87	0.57
36	ER4c	ExonRegion	0	5.92	4.92	8.35	1.81	2.54	4.59	5.95
37	E4_Db	NovelBoundary	0	15.35	5.49	7.20	5.01	4.15	4.07	8.20
38	E4b_E5b	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
39	ER5a	ExonRegion	0	1.54	0.00	0.11	1.03	0.24	0.00	2.73
40	E5_Ab	KnownBoundary	0	1.80	0.00	1.95	1.60	1.08	0.00	6.02
41	ER5b	ExonRegion	0	6.57	3.30	4.76	3.17	3.58	5.58	9.53
42	E5_Da	NovelBoundary	0	4.26	2.31	5.55	9.43	2.01	2.63	2.34
43	E5a_E6a	KnownJunction	0	9.98	6.38	4.86	4.61	2.14	5.55	10.52
44	ER6a	ExonRegion	0	27.16	11.50	16.16	11.26	5.70	11.28	21.53
45	E6a_E7a	KnownJunction	0	18.64	17.10	18.57	8.32	13.83	13.00	32.58
46	ER7a	ExonRegion	0	22.43	12.66	14.33	11.46	7.78	13.91	22.57
47	I7_AR5	ActiveIntronRegion	1	1.54	20.88	3.39	9.98	3.24	27.83	0.00
48	I7_AR6	ActiveIntronRegion	0	1.25	11.81	1.00	4.82	0.31	14.11	0.00
49	I7_SR1	SilentIntronRegion	1	8.41	13.91	9.21	12.19	7.23	9.61	7.52
50	I7_AR1	ActiveIntronRegion	0	9.94	11.99	7.49	12.84	9.07	15.60	6.73
51	ER8a	ExonRegion	0	0.00	0.00	0.00	0.00	1.33	0.00	0.00
52	I8_AR1	ActiveIntronRegion	1	0.73	3.18	3.08	14.60	0.78	6.93	1.67
53	I8_SR2	SilentIntronRegion	1	1.91	2.04	2.64	13.96	1.24	9.39	0.68
54	Ix_AR1	ActiveIntronRegion	0	0.00	4.53	0.68	1.33	4.07	20.14	1.44
55	I8	Intron	1	6.13	9.53	4.14	6.70	5.70	2.41	10.91
56	I8_AR1	ActiveIntronRegion	1	6.51	8.70	5.59	5.87	8.11	1.89	10.83
57	I8_SR1	SilentIntronRegion	1	4.43	13.69	2.64	7.54	3.47	2.12	11.47
58	I8_AR2	ActiveIntronRegion	1	5.73	17.23	2.16	11.22	2.65	1.67	10.00
59	I8_SR2	SilentIntronRegion	1	6.76	9.05	3.23	7.77	4.12	3.25	11.43
60	I8	Intron	1	8.99	8.84	13.13	19.71	21.70	12.76	17.65
61	I8_AR1	ActiveIntronRegion	1	38.01	39.53	59.10	99.97	113.04	64.63	88.19
62	Ix	Intron	1	43.71	5.18	15.67	4.56	3.02	3.48	2.87
63	Ix_SR2	SilentIntronRegion	0	48.50	5.11	16.89	6.33	3.33	3.17	2.42
64	Ix_AR1	ActiveIntronRegion	0	64.96	8.89	23.42	3.62	4.46	6.27	5.70
65	Ix	Intron	0	64.47	20.87	28.99	18.59	22.30	16.16	13.62
66	Ix_SR1	SilentIntronRegion	0	64.63	20.92	29.06	18.64	22.35	16.20	13.66
67	Ix	Intron	1	54.04	3.46	22.38	2.96	2.32	4.65	4.10
68	Ix_SR1	SilentIntronRegion	0	54.17	3.47	22.43	2.97	2.32	4.66	4.11
69	Ix	Intron	1	71.06	8.15	25.80	8.89	4.45	8.81	5.45
70	Ix_AR7	ActiveIntronRegion	0	36.16	3.17	19.21	9.36	2.57	2.85	3.70
71	Ix_AR6	ActiveIntronRegion	0	65.11	8.60	32.29	17.96	0.30	9.99	6.56
72	Ix_AR5	ActiveIntronRegion	0	84.01	11.80	38.35	11.68	4.75	10.61	6.97
73	Ix_SR2	SilentIntronRegion	0	58.09	5.85	22.57	8.21	5.54	5.60	5.38
74	Ix_AR3	ActiveIntronRegion	0	104.41	8.41	23.45	9.09	7.04	13.56	6.70
75	Ix_AR2	ActiveIntronRegion	0	77.06	5.54	16.60	10.99	5.35	14.91	5.58
76	Ix_AR1	ActiveIntronRegion	0	74.94	5.36	24.04	2.81	3.36	4.58	3.83
77	Ix_SR2	SilentIntronRegion	0	27.63	3.77	10.69	1.75	1.69	2.45	3.98
78	Ix	Intron	0	30.91	4.91	13.27	3.56	2.93	3.68	5.05
79	Ix_AR1	ActiveIntronRegion	0	31.03	4.93	13.32	3.57	2.95	3.70	5.07
80	Ix	Intron	0	30.61	5.55	13.95	4.18	5.19	4.32	4.78
81	Ix_AR1	ActiveIntronRegion	0	66.05	12.73	30.60	6.35	5.42	8.74	10.87
82	ER9a	ExonRegion	0	1.28	0.00	0.00	0.00	10.66	0.00	0.00
83	I9_SR4	SilentIntronRegion	0	41.57	28.78	23.15	25.80	18.65	15.05	25.40
84	I9_AR6	ActiveIntronRegion	1	44.40	33.31	25.91	28.89	32.23	21.60	38.67
85	I9_AR9	ActiveIntronRegion	1	38.93	10.71	26.71	12.19	13.20	7.97	28.12
86	I9_AR10	ActiveIntronRegion	0	88.41	26.38	36.91	30.44	24.43	15.53	23.86
87	I9_AR13	ActiveIntronRegion	0	111.64	33.22	87.70	26.44	39.98	33.15	48.79
88	I9_AR14	ActiveIntronRegion	0	88.98	26.77	55.91	31.74	46.99	25.38	36.50
89	I9_AR15	ActiveIntronRegion	0	139.10	18.42	57.37	15.56	38.22	19.09	33.44
90	I9_AR16	ActiveIntronRegion	0	154.76	50.94	97.90	41.84	59.26	47.57	78.84
91	I9_SR14	SilentIntronRegion	1	16.68	9.63	9.81	10.82	7.45	10.19	11.36
92	I9_AR18	ActiveIntronRegion	1	89.55	49.09	42.94	34.92	30.39	27.54	44.82
93	I9_SR15	SilentIntronRegion	1	41.00	32.36	25.69	25.10	20.77	20.68	34.41
94	I9_AR19	ActiveIntronRegion	1	60.94	41.66	31.95	36.28	34.37	35.82	53.37
95	I9_AR20	ActiveIntronRegion	1	42.15	37.52	15.52	25.32	12.77	21.52	20.86
96	I9_AR24	ActiveIntronRegion	1	55.21	27.04	30.22	20.61	39.52	20.75	42.99
97	I9_AR30	ActiveIntronRegion	0	13.20	8.19	13.38	7.78	6.96	8.57	4.64
98	I9_AR31	ActiveIntronRegion	1	28.62	22.77	11.47	19.06	13.34	19.20	19.20
99	I9_AR32	ActiveIntronRegion	1	115.70	31.24	37.16	26.36	62.01	43.61	51.85
100	I9_SR24	SilentIntronRegion	1	63.36	11.99	17.27	16.48	35.55	15.29	34.02
101	I9_AR37	ActiveIntronRegion	1	0.49	0.00	0.34	0.83	0.32	12.93	0.36
102	I9_SR29	SilentIntronRegion	1	11.14	18.18	2.08	0.24	0.00	6.77	0.00
103	I9_AR43	ActiveIntronRegion	1	37.95	80.65	3.71	6.85	2.96	14.01	0.57
104	I9_SR30	SilentIntronRegion	1	12.11	24.72	0.00	2.19	2.57	13.06	0.78
105	I9_AR44	ActiveIntronRegion	1	13.99	38.13	1.04	1.01	0.49	10.25	1.58
106	I9_AR45	ActiveIntronRegion	1	4.82	9.60	0.77	1.21	0.37	2.23	0.24
107	Ix_AR1	ActiveIntronRegion	0	0.91	0.00	0.00	0.00	9.87	0.72	0.79
108	Ix	Intron	0	0.16	0.38	0.11	0.20	7.80	0.48	0.00
109	Ix_AR1	ActiveIntronRegion	0	0.00	0.81	0.00	0.42	8.66	0.00	0.00
110	Ix_SR1	SilentIntronRegion	0	0.21	0.25	0.14	0.13	7.59	0.64	0.00
111	Ix	Intron	0	1.59	0.85	0.00	0.00	11.78	1.73	1.42
112	Ix_AR1	ActiveIntronRegion	0	1.62	0.87	0.00	0.00	11.99	1.76	1.44
113	Ix	Intron	0	0.50	0.00	0.32	0.31	10.94	0.15	0.35
114	Ix_SR1	SilentIntronRegion	0	0.52	0.00	0.23	0.41	8.33	0.00	0.35
115	Ix_AR1	ActiveIntronRegion	0	0.57	0.00	0.84	0.00	26.18	0.86	0.50
116	I9	Intron	0	0.70	1.05	0.26	0.83	21.38	1.86	0.45
117	I9_AR1	ActiveIntronRegion	0	0.27	0.48	0.06	0.81	35.30	1.87	0.18
118	I9_AR2	ActiveIntronRegion	0	2.01	2.90	0.81	1.46	11.61	3.19	1.28
119	ER10a	ExonRegion	0	2.23	0.00	0.27	1.49	7.66	2.91	0.00