Variant report

Variant	rs529615
Chromosome Location	chr3:138313834-138313835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr3:138312701-138313863	Hela-S3	cervix:	n/a	n/a
2	CBX3	chr3:138313178-138313841	K562	blood:	n/a	n/a
3	ZNF143	chr3:138312992-138313849	Hela-S3	cervix:	n/a	chr3:138313129-138313139
4	POLR2A	chr3:138312686-138313913	H1-neurons	neurons:	n/a	n/a
5	MAFK	chr3:138312980-138313934	HepG2	liver:	n/a	chr3:138313608-138313619 chr3:138313608-138313619
6	WRNIP1	chr3:138313320-138314116	GM12878	blood:	n/a	n/a
7	CEBPB	chr3:138313079-138313998	HepG2	liver:	n/a	chr3:138313760-138313771
8	CTCF	chr3:138313328-138313897	H1-hESC	embryonic stem cell:	n/a	n/a
9	RFX5	chr3:138312732-138313885	HepG2	liver:	n/a	chr3:138313432-138313448
10	HCFC1	chr3:138312835-138313856	K562	blood:	n/a	n/a
11	MAX	chr3:138312869-138313923	H1-hESC	embryonic stem cell:	n/a	chr3:138313687-138313697 chr3:138313244-138313254
12	JUND	chr3:138312890-138313905	K562	blood:	n/a	chr3:138313270-138313279
13	CTCF	chr3:138313265-138313835	Fibrobl	skin:	n/a	n/a
14	YY1	chr3:138313520-138313855	A549	lung:	n/a	n/a
15	RAD21	chr3:138313553-138313837	K562	blood:	n/a	n/a
16	CHD2	chr3:138312927-138313966	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr3:138313044-138313964	Spleen_OC	spleen:	n/a	chr3:138313247-138313260
18	POLR2A	chr3:138312537-138313936	PANC-1	pancreas:	n/a	n/a
19	RAD21	chr3:138313340-138313954	Hela-S3	cervix:	n/a	n/a
20	YY1	chr3:138313509-138313834	HepG2	liver:	n/a	n/a
21	CTCF	chr3:138313302-138313837	ProgFib	skin:	n/a	n/a
22	POLR2A	chr3:138312553-138313837	GM18951	blood:	n/a	n/a
23	CTCF	chr3:138313478-138313889	A549	lung:	n/a	n/a
24	USF2	chr3:138313336-138313844	H1-hESC	embryonic stem cell:	n/a	chr3:138313687-138313698
25	CEBPB	chr3:138313111-138314041	K562	blood:	n/a	chr3:138313760-138313771
26	CTCF	chr3:138313330-138313840	GM19238	blood:	n/a	n/a
27	MTA3	chr3:138313175-138313959	GM12878	blood:	n/a	n/a
28	REST	chr3:138312370-138314124	H1-neurons	neurons:	n/a	n/a
29	FOS	chr3:138313587-138313884	MCF10A-Er-Src	breast:	n/a	n/a
30	MAZ	chr3:138312377-138314041	IMR90	lung:	n/a	chr3:138313244-138313254
31	CTCF	chr3:138313429-138313843	Hela-S3	cervix:	n/a	n/a
32	RUNX3	chr3:138312958-138313846	GM12878	blood:	n/a	n/a
33	FOXM1	chr3:138312613-138314067	ECC-1	luminal epithelium:	n/a	n/a
34	BRCA1	chr3:138313631-138313846	HepG2	liver:	n/a	n/a
35	ZNF263	chr3:138312713-138314059	HEK293-T-REx	kidney:	n/a	chr3:138312925-138312934
36	GTF2F1	chr3:138312705-138313857	H1-hESC	embryonic stem cell:	n/a	n/a
37	FOXA1	chr3:138313511-138313910	T-47D	breast:	n/a	n/a
38	MXI1	chr3:138312878-138313861	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr3:138313460-138313864	ECC-1	luminal epithelium:	n/a	n/a
40	RAD21	chr3:138312955-138313944	MCF-7	breast:	n/a	n/a
41	TBP	chr3:138312599-138313959	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOXA1	chr3:138313554-138313868	T-47D	breast:	n/a	n/a
43	RAD21	chr3:138312707-138313973	IMR90	lung:	n/a	n/a
44	SMC3	chr3:138313338-138313932	HepG2	liver:	n/a	chr3:138313442-138313449
45	RAD21	chr3:138313291-138313915	HepG2	liver:	n/a	n/a
46	CTCF	chr3:138313528-138313886	Lung_OC	lung:	n/a	n/a
47	CTCF	chr3:138312363-138314205	SK-N-SH	brain:	n/a	chr3:138313247-138313260 chr3:138312568-138312581
48	ZNF143	chr3:138312946-138313888	H1-hESC	embryonic stem cell:	n/a	chr3:138313129-138313139
49	CREB1	chr3:138312870-138313904	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:138312808-138313923	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:138309173..138314814-chr3:138323140..138328328,8	K562	blood:
2	chr3:138313052..138315422-chr3:138326245..138328582,4	MCF-7	breast:
3	chr3:138313714..138315292-chr3:138315408..138318314,2	K562	blood:
4	chr16:88877584..88878443-chr3:138313223..138314081,2	Hela-S3	cervix:
5	chr3:138311550..138315468-chr3:138324471..138329332,12	MCF-7	breast:
6	chr3:138308688..138311077-chr3:138311353..138314105,2	MCF-7	breast:
7	chr3:138312690..138314858-chr3:138552284..138553853,2	K562	blood:
8	chr3:137892183..137893942-chr3:138313140..138314743,2	K562	blood:
9	chr3:138312928..138314956-chr3:138381208..138383898,2	K562	blood:

Variant related genes	Relation type
CEP70	TF binding region
ENSG00000138231	Chromatin interaction
ENSG00000114107	Chromatin interaction
ENSG00000198931	Chromatin interaction
ENSG00000158234	Chromatin interaction
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1082034	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1082037	0.84[EUR][1000 genomes]
rs1088055	0.81[EUR][1000 genomes]
rs10935282	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10935287	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11709290	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11717771	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916525	0.82[JPT][hapmap]
rs12487652	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487694	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490633	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497070	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630060	0.82[JPT][hapmap]
rs12632794	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12635490	0.86[JPT][hapmap]
rs12635904	0.82[JPT][hapmap]
rs12636246	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12636910	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12637679	0.82[JPT][hapmap]
rs13059817	0.82[JPT][hapmap]
rs13062423	0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13072751	0.81[ASN][1000 genomes]
rs13084780	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13098554	0.82[JPT][hapmap]
rs13098789	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1379257	0.89[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1563615	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1625751	0.85[ASN][1000 genomes]
rs1672927	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1672928	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1672931	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1672932	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1672933	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1672936	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1672938	0.83[EUR][1000 genomes]
rs1672939	0.81[EUR][1000 genomes]
rs1672963	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673593	0.86[EUR][1000 genomes]
rs1673594	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673607	0.89[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1673608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673622	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673624	0.88[EUR][1000 genomes]
rs1679167	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1679169	0.83[AMR][1000 genomes]
rs1720833	0.85[ASN][1000 genomes]
rs1720836	0.89[TSI][hapmap]
rs2086351	0.85[ASN][1000 genomes]
rs2348146	0.88[EUR][1000 genomes]
rs2607790	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2607795	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs28719641	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2881793	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs34377792	0.80[ASN][1000 genomes]
rs34583117	0.80[ASN][1000 genomes]
rs35471402	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35500947	0.88[ASN][1000 genomes]
rs35932955	0.86[ASN][1000 genomes]
rs361073	0.81[TSI][hapmap]
rs361075	0.81[TSI][hapmap]
rs361077	0.81[TSI][hapmap]
rs3813264	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs3884240	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3884241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4432674	0.86[EUR][1000 genomes]
rs4678266	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs484698	0.81[TSI][hapmap]
rs4894389	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs497334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs503922	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537210	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs542010	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs550507	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs559313	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs56394118	0.87[ASN][1000 genomes]
rs564800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579750	0.83[EUR][1000 genomes]
rs582386	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586946	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs587005	0.88[EUR][1000 genomes]
rs587331	0.87[EUR][1000 genomes]
rs609497	0.83[EUR][1000 genomes]
rs609797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs611134	0.89[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs612471	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618792	0.83[EUR][1000 genomes]
rs620035	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs629884	0.89[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs634374	0.87[EUR][1000 genomes]
rs6439809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6439810	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654528	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs656107	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664928	0.88[EUR][1000 genomes]
rs66775405	0.81[ASN][1000 genomes]
rs6762114	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6763380	0.85[CEU][hapmap]
rs6771237	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6798058	0.88[EUR][1000 genomes]
rs680070	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs73229526	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7625326	0.89[CEU][hapmap]
rs7626226	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7627685	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs7634745	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs7643973	0.89[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7645920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653815	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs773443	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs773444	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs773445	0.84[EUR][1000 genomes]
rs773448	0.82[EUR][1000 genomes]
rs773449	0.84[EUR][1000 genomes]
rs773450	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs773452	0.86[EUR][1000 genomes]
rs773455	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs774011	0.85[ASN][1000 genomes]
rs774012	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs811322	0.83[TSI][hapmap]
rs814022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9049	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs936316	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9681127	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9811052	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9817419	0.89[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9822037	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9823182	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848718	0.88[CEU][hapmap]
rs9848938	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9855306	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9878436	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs529615	MSL2	cis	cerebellum	SCAN
rs529615	FAIM	cis	multi-tissue	Pritchard
rs529615	FAIM	cis	parietal	SCAN
rs529615	FAIM	cis	cerebellum	SCAN
rs529615	FAIM	cis	Muscle Skeletal	GTEx
rs529615	ESYT3	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138311600-138315000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:138311800-138314000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:138311800-138314000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:138312000-138314000	Active TSS	Fetal Brain Female	brain
5	chr3:138312000-138314000	Active TSS	Fetal Kidney	kidney
6	chr3:138312200-138314000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:138312400-138314000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr3:138312400-138314000	Active TSS	Stomach Mucosa	stomach
9	chr3:138312400-138314000	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:138312600-138314000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:138312600-138314000	Active TSS	Fetal Lung	lung
12	chr3:138312600-138314000	Active TSS	Thymus	Thymus
13	chr3:138312800-138314200	Flanking Active TSS	Dnd41	blood
14	chr3:138313000-138314000	Active TSS	Primary T cells from cord blood	blood
15	chr3:138313000-138314000	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:138313200-138314000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:138313400-138314000	Flanking Active TSS	Hela-S3	cervix
18	chr3:138313400-138314000	Flanking Active TSS	Osteobl	bone
19	chr3:138313400-138314200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:138313600-138314000	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr3:138313600-138314000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:138313600-138314000	Enhancers	Gastric	stomach
23	chr3:138313600-138314000	Enhancers	Lung	lung
24	chr3:138313600-138314000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:138313600-138327200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:138313800-138314000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:138313800-138314000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:138313800-138314000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:138313800-138314000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:138313800-138314000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:138313800-138314000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:138313800-138314000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:138313800-138314000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:138313800-138314000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:138313800-138314000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:138313800-138314000	Enhancers	Primary B cells from peripheral blood	blood
37	chr3:138313800-138314000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:138313800-138314000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:138313800-138314000	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:138313800-138314000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:138313800-138314000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:138313800-138314000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:138313800-138314000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:138313800-138314000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:138313800-138314000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:138313800-138314000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:138313800-138314000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr3:138313800-138314000	Flanking Active TSS	Liver	Liver
49	chr3:138313800-138314000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:138313800-138314000	Flanking Active TSS	Brain Cingulate Gyrus	brain

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