Supplementary Table 4. Methylation sites between iC1 and iC3 subtypes.
ID	iC1_MetHyper	iC3_MetHyper	iC1_MetHypo	iC3_MetHypo	iC1_Normal	iC3_Normal	FisherP	gName
cg14646111	3	66	7	0	20	16	6.78020270879965e-13	SEC23B
cg06377278	1	0	11	81	18	1	6.91126894624679e-13	RUNX3
cg12008047	2	54	12	0	16	28	1.97651729961952e-12	GDF15
cg03774514	0	0	26	12	4	70	2.04005742718707e-12	FOXA2
cg14611152	0	0	4	69	26	13	5.80382677045611e-12	DAB2IP
cg19506201	6	73	2	0	22	9	7.04989714831330e-12	ASPSCR1
cg07104895	7	74	2	0	21	8	1.80744875846408e-11	ASPSCR1
cg10087374	24	10	0	0	6	72	2.22322302253071e-11	FAM160B2
cg16539629	0	0	10	78	20	4	3.13785306391803e-11	C14orf132
cg04597312	2	29	15	0	13	53	3.59134349321647e-11	IRF8
cg06591466	0	0	10	77	20	5	1.39970910901199e-10	C14orf132
cg04184208	1	0	11	78	18	4	2.12365831075891e-10	C14orf132
cg11698119	0	47	3	0	27	35	2.88480510784506e-10	KRT18
cg21138752	0	0	28	23	2	59	3.84743360550331e-10	ZSCAN31
cg06903569	0	4	28	23	2	55	4.8075996360184e-10	ZSCAN31
cg02573468	1	13	14	0	15	69	1.00751678423739e-09	DLL4
cg23084951	0	3	28	24	2	55	1.04749415625051e-09	ZSCAN31
cg19013262	0	0	28	25	2	57	1.05519910009356e-09	ZSCAN31
cg26970841	0	0	28	25	2	57	1.05519910009356e-09	IRF8
cg05490983	0	0	28	25	2	57	1.05519910009356e-09	CLDN7
cg25084393	0	7	21	8	9	67	1.18961684677845e-09	CTPS2
cg23505344	0	0	12	78	18	4	1.32124092179498e-09	C14orf132
cg05906607	0	0	12	78	18	4	1.32124092179498e-09	C14orf132
cg13997124	0	4	28	24	2	54	1.61285857199254e-09	ZSCAN31
cg18674899	3	60	0	0	27	22	1.85990298674101e-09	RWDD2A
cg09996797	0	1	28	26	2	55	3.10044586355778e-09	ZSCAN31
cg09030848	2	56	0	0	28	26	3.10044586355785e-09	ZFYVE21
cg03978375	0	0	28	26	2	56	3.10044586355785e-09	IRF8
cg17968647	0	0	28	26	2	56	3.10044586355785e-09	ZSCAN31
cg19119071	0	0	29	31	1	51	4.37171104563234e-09	RWDD2A
cg20396393	1	12	13	0	16	70	4.45061590017079e-09	FAM221A
cg12293132	0	0	28	27	2	55	4.56634859630268e-09	FAM221A
cg08343881	0	3	28	26	2	53	4.96897835055609e-09	ZSCAN31
cg05605299	0	2	28	26	2	54	5.01639114111117e-09	ZSCAN31
cg06671706	0	0	21	10	9	72	7.82135072480675e-09	CLDN23
cg02399455	4	60	2	0	24	22	9.61574417957434e-09	SRI
cg17744110	5	63	0	0	25	19	9.93636337944222e-09	CALM3
cg25639095	9	71	2	0	19	11	1.14617714404678e-08	ENGASE
cg04749631	0	5	29	31	1	46	1.38467864797975e-08	RWDD2A
cg12169661	0	0	12	0	18	82	1.95823163856074e-08	CLDN3
cg27208925	20	10	1	1	9	71	2.03605776343054e-08	IRF8
cg24826867	0	0	28	30	2	52	2.96610742896926e-08	IRF8
cg04554272	2	42	7	0	21	40	4.85076749975221e-08	LMF1
cg04799958	0	0	21	12	9	70	5.00367479867879e-08	KRT18
cg08690876	0	0	15	3	15	79	5.01724155806312e-08	CYB5R3
cg24277817	3	3	16	6	11	73	5.70470839983601e-08	NFIX
cg11798857	0	0	28	31	2	51	7.19446241349304e-08	FOXA2
cg05331498	0	0	17	6	13	76	9.59509352020867e-08	IL17RB
cg00117172	1	0	13	76	16	6	9.59509352020869e-08	RUNX3
cg02239805	0	0	14	77	16	5	1.46413281638196e-07	MDFIC
cg10500512	0	0	29	37	1	45	1.77253621214088e-07	FOXA2
cg01270466	0	0	18	81	12	1	2.12272309619993e-07	C14orf132
cg14644871	0	0	30	43	0	39	2.20253300716209e-07	NFE2L3
cg21211585	0	0	17	7	13	75	2.83918776595625e-07	GDF15
cg21699330	0	2	29	37	1	43	4.72560891077459e-07	NFE2L3
cg13049997	5	56	2	0	23	26	5.69571615796278e-07	SFT2D1
cg12685560	0	0	20	13	10	69	5.7735946732701e-07	MNT
cg15743358	0	0	24	22	6	60	6.35071022932152e-07	ZSCAN31
cg12636882	6	60	0	0	24	22	6.35071022932152e-07	HTT
cg13537416	3	29	9	0	18	53	7.59411333819059e-07	DAB2IP
cg19590532	0	0	13	74	17	8	7.6451837106773e-07	RUNX3
cg02052762	12	2	1	14	17	66	1.09122058593325e-06	ANKFY1
cg19757309	0	0	17	79	13	3	1.16660245886751e-06	C14orf132
cg14212748	0	0	12	2	18	80	1.23703272818464e-06	KRT18
cg15390413	0	0	27	33	3	49	1.49908079097096e-06	CHRNB1
cg25258033	1	2	9	0	20	80	2.06057500788128e-06	RNASET2
cg14594111	8	0	1	0	21	82	2.60387386098597e-06	DAB2IP
cg25200151	7	60	0	0	23	22	2.78054967429614e-06	ACAD10
cg23401436	10	67	0	0	20	15	3.88699890975854e-06	HNRNPA2B1
cg24419391	2	11	9	0	19	71	4.70676772263617e-06	CLDN3
cg09984479	0	0	10	1	20	81	4.79880122752775e-06	TMEM184B
cg00541544	0	1	26	31	4	50	5.89053762412976e-06	SUN2
cg10155875	0	0	28	39	2	43	6.4880936422001e-06	IRF8
cg15695585	1	1	17	77	12	4	6.59463154208756e-06	MDFIC
cg27650175	4	1	19	80	7	1	8.29003965757688e-06	DAB2IP
cg14986962	0	1	28	38	2	43	8.53547581137403e-06	IRF8
cg14063008	2	0	19	80	9	2	8.56386227954152e-06	DAB2IP
cg03207391	1	38	0	0	29	44	9.2609413645578e-06	GDF15
cg06946838	0	0	13	71	17	11	9.61654916514507e-06	MDFIC
cg03639917	0	0	13	71	17	11	9.61654916514507e-06	MUC3A
cg12640656	0	0	25	29	5	53	1.03911903167514e-05	TBC1D14
cg22814048	0	1	30	50	0	31	1.15798430023297e-05	RWDD2A
cg02248763	3	38	11	5	16	39	1.22818491584242e-05	DUSP8
cg06744585	5	18	14	6	11	58	1.88263477696095e-05	NFIX
cg07730007	12	69	0	0	18	13	1.9515105686616e-05	MTERF2
cg11630135	13	70	0	0	17	12	1.98927272250853e-05	FBLN2
cg20354141	0	0	21	81	9	1	2.12607564765943e-05	MUC3A
cg07652628	0	1	11	3	19	78	2.13726760403325e-05	KRT18
cg13147246	14	7	0	0	16	75	2.13875809694167e-05	YBX2
cg12963560	0	0	29	46	1	36	2.21091944760085e-05	MAP7
cg24866784	1	36	0	0	29	46	2.21091944760085e-05	FBLN2
cg12510708	0	0	23	25	7	57	2.41883681089346e-05	NFE2L3
cg04091702	0	0	15	9	15	73	2.9799345300178e-05	MARVELD2
cg21005416	0	0	23	26	7	56	2.99191416335532e-05	ECE1
cg22635885	0	28	1	0	29	54	3.22372943817503e-05	CTPS2
cg15069235	1	18	6	0	23	64	3.2940125974058e-05	HDAC2
cg12700904	0	0	10	63	20	19	3.66081274494502e-05	FBLN2
cg17340373	0	29	0	0	30	53	4.21129481070824e-05	FBLN2
cg14055351	16	74	0	0	14	8	4.92832530833432e-05	CSNK1E
cg18857889	0	0	17	13	13	69	5.34148529427626e-05	FAM221A
cg27191921	0	0	7	0	23	82	5.61942738378801e-05	CYB5R3
cg27052455	11	65	0	0	19	17	5.62354444213561e-05	ENGASE
cg03840849	0	0	17	14	13	68	8.30844078497447e-05	AC005083.1
cg14869505	6	51	0	0	24	31	9.18646992976561e-05	ATP5B
cg26485825	0	0	9	2	21	80	9.53395550973856e-05	LAMA3
cg01651570	21	80	0	0	9	2	9.53395550973856e-05	ZFYVE21
cg18406197	0	0	10	62	20	20	9.59612553646268e-05	FBLN2
cg11851174	12	6	0	2	18	74	0.000147899140069557	RAI1
cg08128768	1	0	17	74	12	8	0.000170711472873374	DAB2IP
cg25151916	0	0	22	26	8	56	0.000176343813182851	YBX2
cg24704593	0	0	26	39	4	43	0.00018654547878237	AC005083.1
cg04918082	0	0	23	29	7	53	0.000202071224609678	MUC3A
cg19655557	16	72	0	0	14	10	0.000211121180873025	CCDC127
cg04809787	0	0	24	33	6	49	0.000231123806190213	CHRNB1
cg20737812	0	13	8	3	22	66	0.000290832600442484	KLHL25
cg17359753	0	0	9	3	21	79	0.000310485900926746	AKT2
cg26168469	0	0	23	81	7	1	0.000363389637484958	C14orf132
cg15200445	0	1	8	2	22	79	0.000364717004627534	PIP5K1C
cg25044876	0	0	8	2	22	80	0.000364717004627555	CYB5R3
cg07652237	0	0	30	59	0	23	0.000391924666641529	PHF10
cg23160483	28	48	0	0	2	34	0.000436441570841332	ASPSCR1
cg15792487	0	0	24	34	6	48	0.000502045217603292	CHRNB1
cg10989517	0	0	18	19	12	63	0.000506031373660046	SERGEF
cg12795893	0	0	24	35	6	47	0.000542237705607955	ATP5B
cg18884137	0	0	21	27	9	55	0.000568792844299698	CHRNB1
cg16600934	9	55	0	0	21	27	0.000568792844299698	AKT1
cg01194538	1	0	9	5	20	77	0.000588268084932837	CYB5R3
cg23306063	20	77	0	0	10	5	0.000588268084932837	TYK2
cg01989521	1	1	6	1	23	80	0.000602647564940836	CDC42BPB
cg15054077	0	0	27	45	3	37	0.000645950193825098	NFIX
cg16929104	0	0	30	60	0	22	0.000775969625126859	GDF15
cg07495470	0	0	9	4	21	78	0.000820382740542355	POLDIP3
cg16419724	0	0	11	7	19	75	0.000851490890263224	MARVELD2
cg18421949	9	4	3	22	18	56	0.000935531974327744	MAP7
cg01819995	17	72	0	0	13	10	0.000945667331160571	PDRG1
cg16759783	0	0	13	10	17	72	0.000945667331160571	TXNL4A
cg00950244	0	0	5	0	25	82	0.00106225908978204	NDUFAF4
cg08839186	6	45	0	0	24	37	0.00119475564049391	FBLN2
cg15696816	23	34	0	0	7	48	0.00123435109322254	RAI1
cg15298719	0	0	7	2	23	80	0.0013204213473085	CLDN7
cg20000088	9	53	0	0	21	29	0.00133720764008853	FBLN2
cg09709600	27	48	0	0	3	34	0.00141671847655515	EHBP1L1
cg05406678	0	3	7	2	23	77	0.00142995039609427	CCDC127
cg23712530	8	50	0	0	22	32	0.00145744226751873	TECPR2
cg10017888	0	0	30	62	0	20	0.00150229771602383	CALM3
cg19142553	2	18	4	0	24	64	0.00182172769178868	HNRNPA2B1
cg17156534	0	0	26	45	4	37	0.00186021221357685	TOP1
cg08470764	0	0	21	77	9	5	0.00186489869078522	MUC3A
cg01896761	9	8	8	50	13	24	0.00190279009011649	FBLN2
cg02968914	2	29	0	0	28	53	0.00191471458471866	CSNK1G2
cg06998965	0	0	29	57	1	25	0.00192557945771472	MARVELD2
cg10536999	0	1	30	62	0	19	0.00195542194870115	NFE2L3
cg26242531	0	0	14	13	16	69	0.00206962438104978	ZFYVE21
cg06418871	0	0	29	58	1	24	0.00214426433895632	MARVELD2
cg18672959	0	0	25	42	5	40	0.00222878658898567	CHRNB1
cg10795659	0	3	25	40	5	39	0.00243658028824939	TMEM171
cg11616676	0	1	29	57	1	24	0.00246528511510236	SRI
cg07103895	24	39	0	0	6	43	0.00248790771163902	C14orf79
cg24794433	0	0	16	68	14	14	0.00262415362920437	DAB2IP
cg06761850	0	0	20	28	10	54	0.00262617078227424	TECPR2
cg21937244	3	32	0	0	27	50	0.00281945011747004	CDC42BPB
cg04887278	0	0	30	64	0	18	0.00291462216217218	RWDD2A
cg02817981	0	1	11	8	19	73	0.00305949561027739	HSPD1
cg18603228	1	0	9	50	20	32	0.0031615966261825	FBLN2
cg20950843	0	15	1	0	29	67	0.00324308946649203	CYB5R3
cg03818715	0	3	13	11	17	68	0.00331053393204001	SNRNP48
cg06983112	28	54	0	0	2	28	0.00336210621557588	FBXL19
cg19436804	15	66	0	0	15	16	0.00347775255015945	CLDN23
cg11249241	0	0	15	66	15	16	0.00347775255015945	NFIX
cg11358945	12	11	0	0	18	71	0.00356335992706878	NR4A2
cg05901765	0	0	29	59	1	23	0.00369684610334804	MARVELD2
cg25731807	0	0	29	59	1	23	0.00369684610334804	TMEM171
cg16126178	21	76	0	0	9	6	0.00377984459956396	AKT1
cg13110239	0	0	9	6	21	76	0.00377984459956396	CSNK1E
cg09427156	12	58	0	0	18	24	0.00412500961460062	ATP5B
cg24629380	3	23	3	0	24	59	0.00419286775383769	VANGL1
cg19589358	26	82	0	0	4	0	0.00441246083447912	CDC42BPB
cg11425201	26	82	0	0	4	0	0.00441246083447912	AKT2
cg06683487	13	13	0	0	17	69	0.00456927996715222	LMF1
cg14542590	19	27	0	0	11	55	0.00491954604946579	FOXN3
cg02315870	2	12	4	0	24	70	0.00509065084106513	HNRNPA2B1
cg01346718	0	0	5	1	25	81	0.00513259765810597	CSNK1E
cg24018841	25	81	0	0	5	1	0.00513259765810597	MKKS
cg18757468	7	44	0	0	23	38	0.00523774481975395	EHBP1L1
cg07946961	7	44	0	0	23	38	0.00523774481975395	CSNK1G2
cg09330078	23	38	0	0	7	44	0.00523774481975395	TNKS1BP1
cg00306510	22	77	0	0	8	5	0.00552070451663526	TLR3
cg02780743	0	0	30	65	0	17	0.00554488197934228	GDF15
cg04809453	9	6	7	17	14	59	0.00555495245866206	LMF1
cg18817426	0	0	20	30	10	52	0.00555727234643004	COX5A
cg16076328	0	0	20	30	10	52	0.00555727234643004	EPCAM
cg13461622	19	26	0	2	11	54	0.00568820420736321	RUNX3
cg13060154	0	0	14	62	16	20	0.00578021878543804	DAB2IP
cg23989110	10	51	1	0	19	31	0.00600637216540988	MAP3K6
cg02021919	7	42	1	0	22	40	0.00603101356142412	CCNH
cg01259871	8	45	1	0	21	37	0.00627402011316343	POLR3H
cg07115761	28	56	0	0	2	26	0.00631473031569589	AXIN1
cg25502086	0	0	28	55	2	27	0.00632084135499973	AIFM2
cg05726661	0	0	17	22	13	60	0.00648080347104514	CHRNB1
cg03210866	0	0	17	22	13	60	0.00648080347104514	EPCAM
cg02087954	0	0	20	74	10	8	0.00669022427612998	MUC3A
cg23526147	0	0	14	16	16	66	0.00723818826697157	NFIX
cg24479590	0	2	24	40	6	40	0.00743540687538687	CHRNB1
cg27058497	8	5	0	2	22	75	0.00779235541050842	RUNX3
cg07489003	1	18	1	0	28	64	0.00831003541513241	XK
cg10868156	19	28	0	0	11	54	0.00890775794571273	RAI1
cg04987122	2	2	3	0	25	80	0.00891287291190925	TRAF7
cg13908507	15	18	0	0	15	64	0.00899452527968597	AIFM2
cg12339328	20	73	0	0	10	9	0.00933431425356918	SEC23B
cg23931049	0	0	10	9	20	73	0.00933431425356918	LAMA3
cg00194126	20	31	0	0	10	51	0.00970276358292959	NR4A2
cg02842158	20	31	0	0	10	51	0.00970276358292959	LMF2
cg09256201	0	0	12	13	18	69	0.0101760782676283	HAAO
cg16673929	0	0	20	32	10	50	0.0109894387789064	NFIX
cg06801852	21	75	0	0	9	7	0.0113808805396175	JAG2
cg02505827	0	0	28	58	2	24	0.0115854535131916	MARVELD2
cg27085869	0	0	29	62	1	20	0.0123031028323916	TMEM171
cg21032150	0	0	29	62	1	20	0.0123031028323916	COMMD7
cg14274896	0	0	29	63	1	19	0.0130182793952955	FUCA2
cg19555986	0	0	29	63	1	19	0.0130182793952955	MAP7
cg22637538	0	4	22	35	8	43	0.0134289742987747	CHRNB1
cg07002422	19	71	0	0	11	11	0.0134612133598655	LMF1
cg17329670	0	0	25	80	5	2	0.0144636568288863	PSTPIP2
cg02943420	25	80	0	0	5	2	0.0144636568288863	ZFYVE21
cg00460818	5	34	0	0	25	48	0.0150163537153367	C14orf79
cg09103877	25	48	0	0	5	34	0.0150163537153367	RAI1
cg02694489	0	0	13	16	17	66	0.0151522283034737	CHRNB1
cg03186999	0	0	27	55	3	27	0.0161531020537664	CLDN7
cg04215179	0	0	23	41	7	41	0.0169699118431364	FAM221A
cg03634729	0	0	3	0	27	82	0.0178132678132676	LAMA3
cg20267398	27	82	0	0	3	0	0.0178132678132676	HSPD1
cg19248564	0	0	3	0	27	82	0.0178132678132676	CYB5R3
cg08800497	27	82	0	0	3	0	0.0178132678132676	CSNK1G2
cg13516541	27	82	0	0	3	0	0.0178132678132676	AKT1
cg11864882	0	0	26	81	4	1	0.017813267813268	PSTPIP2
cg20670302	0	0	26	81	4	1	0.017813267813268	PSTPIP2
cg10099364	0	0	30	69	0	13	0.0186507009006438	AHCY
cg26600954	0	0	30	69	0	13	0.0186507009006438	FAM221A
cg22120345	0	0	30	68	0	14	0.0195463218854112	FAM221A
cg14042504	0	0	30	68	0	14	0.0195463218854112	FOXA2
cg17290213	0	0	4	30	26	52	0.0203756478699581	EHBP1L1
cg23714481	0	0	2	22	28	60	0.0207595845731156	C14orf79
cg26776924	18	68	0	0	12	14	0.0209957684217848	CSNK1G2
cg09028855	1	12	2	0	27	70	0.0232977494237	EIF2S2
cg23928512	14	59	0	0	16	23	0.0239203683848457	ASPSCR1
cg10013142	5	34	1	1	24	47	0.0239666892693302	ZFYVE21
cg19440264	12	15	0	0	18	67	0.0246640041396728	CHRNB1
cg11276600	5	31	1	0	24	51	0.0252897672879143	HDAC2
cg20398418	20	71	0	0	10	11	0.0270208847732296	NR4A2
cg04803994	0	0	27	56	3	26	0.027044086515502	DUSP8
cg20320656	0	0	24	46	6	36	0.0271047524564906	LETMD1
cg06748147	0	0	27	57	3	25	0.0281354517520561	CSNK1E
cg08387551	0	6	2	0	28	76	0.02827428267742	TMEM171
cg05427639	1	5	23	40	6	37	0.0285343925635397	NT5C3A
cg11758861	0	0	23	43	7	39	0.0294296215157129	NFIX
cg07815521	1	3	3	0	26	79	0.0296343817105334	AKT2
cg16851482	0	1	5	3	25	78	0.0310522064658274	TBC1D14
cg02049499	0	0	25	79	5	3	0.0310522064658282	LMF1
cg26521207	0	0	5	3	25	79	0.0310522064658282	CYCS
cg06530012	0	0	25	79	5	3	0.0310522064658282	PSTPIP2
cg06494844	25	79	0	0	5	3	0.0310522064658282	ENGASE
cg00240195	22	41	0	0	8	41	0.0325505633945803	NR4A2
cg04817870	28	59	0	1	2	22	0.0325767270758256	ASPSCR1
cg17800442	0	0	22	74	8	8	0.0333018706588523	CTF1
cg09368936	0	0	22	74	8	8	0.0333018706588523	HAAO
cg17352995	0	0	28	61	2	21	0.0338752771493971	SH3TC1
cg01275566	0	12	0	0	30	70	0.0339614482752104	DLG5
cg16227775	0	0	30	70	0	12	0.0339614482752104	ABCB7
cg00816609	0	12	0	0	30	70	0.0339614482752104	FBLN2
cg23279136	0	0	30	71	0	11	0.0345509342100665	ABCB7
cg22971216	0	0	30	71	0	11	0.0345509342100665	EPCAM
cg11195733	19	69	0	0	11	13	0.0349632134153985	TECPR2
cg06206957	0	3	24	43	6	36	0.0366912096752665	NT5C3A
cg05448137	19	68	0	0	11	14	0.0396135103004334	ASPSCR1
cg17525856	0	0	16	61	14	21	0.0403284651970545	EPCAM
cg14085715	0	1	28	60	2	21	0.0403852737021094	AC005083.1
cg05656688	11	12	0	3	19	67	0.0410753086620931	RUNX3
cg20792436	3	3	4	3	23	76	0.0414113062445433	ASPSCR1
cg05804949	0	1	30	70	0	11	0.0418869994124393	FAM221A
cg13768737	0	0	26	80	4	2	0.0431746081235934	PSTPIP2
cg02384115	0	0	26	80	4	2	0.0431746081235934	CLDN12
cg27541863	26	80	0	0	4	2	0.0431746081235934	ATP5B
cg07236781	27	58	0	0	3	24	0.0452230242978348	RUNX3
cg07566286	12	16	0	0	18	66	0.0466103072074837	MAPK8IP1
cg06544989	7	37	0	0	23	45	0.0489998668420261	GTPBP1