Variant report

Variant	rs3758505
Chromosome Location	chr10:94334778-94334779
allele	G/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	CTCF	chr10:94334760-94334910	AG09309	skin:	n/a	n/a
2	CTCF	chr10:94334760-94334910	NHEK	skin:	n/a	n/a
3	GATA1	chr10:94332030-94334836	PBDE	blood:	n/a	chr10:94334273-94334284 chr10:94332190-94332207 chr10:94334317-94334328
4	CTCF	chr10:94333631-94335070	K562	blood:	n/a	chr10:94334198-94334206
5	MXI1	chr10:94332907-94334916	GM12878	blood:	n/a	n/a
6	MYC	chr10:94333523-94334986	MCF10A-Er-Src	breast:	n/a	chr10:94334346-94334355
7	CTCF	chr10:94334740-94334890	HCT-116	colon:	n/a	n/a
8	RAD21	chr10:94333803-94334789	H1-hESC	embryonic stem cell:	n/a	chr10:94334366-94334376
9	CTCF	chr10:94334760-94334910	HAc	cerebellar:	n/a	n/a
10	RAD21	chr10:94333525-94334869	IMR90	lung:	n/a	chr10:94334366-94334376
11	RAD21	chr10:94333501-94335231	SK-N-SH	brain:	n/a	chr10:94334366-94334376
12	CTCF	chr10:94333762-94335086	GM12878	blood:	n/a	chr10:94334198-94334206
13	POLR2A	chr10:94334611-94334899	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr10:94334680-94334830	A549	lung:	n/a	n/a
15	MYC	chr10:94332784-94334952	MCF10A-Er-Src	breast:	n/a	chr10:94334346-94334355 chr10:94333410-94333419
16	MAX	chr10:94332697-94334946	NB4	blood:	n/a	chr10:94334346-94334355 chr10:94333410-94333419
17	SMC3	chr10:94333524-94334999	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr10:94332390-94335273	A549	lung:	n/a	chr10:94334198-94334206 chr10:94332811-94332820
19	CTCF	chr10:94333654-94334998	IMR90	lung:	n/a	chr10:94334198-94334206
20	RELA	chr10:94333601-94334969	GM18505	blood:	n/a	n/a
21	CTCF	chr10:94334660-94334810	HVMF	connective:	n/a	n/a
22	RFX5	chr10:94333428-94335058	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr10:94334720-94334870	WI-38	lung:	n/a	n/a
24	POLR2A	chr10:94334700-94335035	HepG2	liver:	n/a	n/a
25	CTCF	chr10:94334740-94334890	HBMEC	blood vessel:	n/a	n/a
26	FOS	chr10:94334587-94335113	MCF10A-Er-Src	breast:	n/a	n/a
27	ZKSCAN1	chr10:94332289-94334804	Hela-S3	cervix:	n/a	n/a
28	KAP1	chr10:94333585-94334909	HEK293	kidney:	n/a	n/a
29	ZNF143	chr10:94334218-94335004	Hela-S3	cervix:	n/a	n/a
30	SIN3A	chr10:94332811-94334909	H1-hESC	embryonic stem cell:	n/a	chr10:94333878-94333887
31	MXI1	chr10:94331962-94335157	SK-N-SH	brain:	n/a	n/a
32	MTA3	chr10:94332542-94334854	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr10:94332784-94335135	MCF-7	breast:	n/a	n/a
34	CTCF	chr10:94334703-94335109	MCF-7	breast:	n/a	n/a
35	NRF1	chr10:94333492-94334881	SK-N-SH	brain:	n/a	chr10:94333841-94333855 chr10:94333844-94333855 chr10:94333669-94333676 chr10:94333843-94333854
36	CTCF	chr10:94332258-94335100	SK-N-SH	brain:	n/a	chr10:94334198-94334206 chr10:94332811-94332820
37	CTCF	chr10:94334680-94334830	RPTEC	kidney:	n/a	n/a
38	GTF2F1	chr10:94333639-94335056	Hela-S3	cervix:	n/a	n/a
39	BRCA1	chr10:94333593-94334908	Hela-S3	cervix:	n/a	n/a
40	JUND	chr10:94333505-94334786	H1-hESC	embryonic stem cell:	n/a	chr10:94333898-94333912 chr10:94334026-94334037
41	ZNF263	chr10:94332394-94334944	HEK293-T-REx	kidney:	n/a	n/a
42	WRNIP1	chr10:94333789-94334863	GM12878	blood:	n/a	n/a
43	FOS	chr10:94334536-94335022	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:94327650..94337583-chr10:94349444..94356782,22	K562	blood:
2	chr10:94334145..94336156-chr10:94441112..94444728,3	K562	blood:
3	chr10:94300885..94308768-chr10:94330971..94336052,7	K562	blood:
4	chr10:94330286..94336827-chr10:94349891..94354260,15	K562	blood:
5	chr10:94334190..94336878-chr10:94340281..94341907,2	K562	blood:
6	chr10:94332371..94335153-chr10:94446165..94448467,2	K562	blood:
7	chr10:94332956..94335217-chr10:94607050..94609174,2	MCF-7	breast:
8	chr10:94332262..94336114-chr10:94349834..94354042,11	MCF-7	breast:
9	chr10:94333639..94335354-chr10:94637611..94639541,2	MCF-7	breast:
10	chr10:94332407..94336018-chr10:94349212..94353201,7	MCF-7	breast:
11	chr10:94333616..94336720-chr10:94448718..94451044,3	K562	blood:

Variant related genes	Relation type
IDE	TF binding region
ENSG00000138160	Chromatin interaction
ENSG00000119912	Chromatin interaction
ENSG00000225118	Chromatin interaction
ENSG00000152804	Chromatin interaction
ENSG00000138190	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10882066	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882069	0.84[ASN][1000 genomes]
rs10882078	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882084	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs10882086	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882088	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882093	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11186999	0.86[ASN][1000 genomes]
rs11187013	0.85[ASN][1000 genomes]
rs11187018	0.84[EUR][1000 genomes]
rs11187034	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11187037	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11187060	0.81[JPT][hapmap]
rs11187077	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11187079	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187092	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11187108	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187115	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11595187	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12218324	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12218329	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12411517	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12411873	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12414433	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415807	0.86[ASN][1000 genomes]
rs12416180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17107734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1832197	0.81[JPT][hapmap]
rs1999763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275219	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297743	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421940	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35118791	0.81[ASN][1000 genomes]
rs3758503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646954	0.94[ASW][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646958	0.81[ASN][1000 genomes]
rs4933232	0.86[ASN][1000 genomes]
rs4933728	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4933731	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4933732	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57936176	0.81[ASN][1000 genomes]
rs6583820	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7068118	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7068618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7075073	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7075851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7078413	0.85[JPT][hapmap]
rs7079099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7087153	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7089987	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7093437	0.86[ASN][1000 genomes]
rs7097800	0.89[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs74151674	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7895832	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs7898114	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7898862	0.86[ASN][1000 genomes]
rs7900584	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910605	0.93[GIH][hapmap];0.85[JPT][hapmap]
rs7916460	0.81[ASN][1000 genomes]
rs7916594	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	esv1792868	chr10:94232247-94409749	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv895894	chr10:94249982-94452430	Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv895895	chr10:94304132-94372706	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94332000-94334800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr10:94332200-94334800	Active TSS	HSMM	muscle
3	chr10:94332200-94335000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:94332400-94334800	Active TSS	Aorta	Aorta
5	chr10:94332400-94334800	Active TSS	Colonic Mucosa	Colon
6	chr10:94332400-94335000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr10:94332400-94335000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:94332600-94334800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:94332600-94334800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr10:94332600-94334800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr10:94332600-94334800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr10:94332600-94334800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:94332600-94334800	Bivalent/Poised TSS	HepG2	liver
14	chr10:94332600-94335000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr10:94332600-94335000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:94332600-94335000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr10:94332600-94335000	Active TSS	Stomach Mucosa	stomach
18	chr10:94332800-94334800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr10:94332800-94334800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:94332800-94334800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr10:94332800-94334800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:94332800-94334800	Active TSS	Ovary	ovary
23	chr10:94332800-94334800	Active TSS	Right Ventricle	heart
24	chr10:94332800-94334800	Active TSS	Small Intestine	intestine
25	chr10:94332800-94334800	Active TSS	NHDF-Ad	bronchial
26	chr10:94332800-94335000	Active TSS	Esophagus	oesophagus
27	chr10:94332800-94335000	Active TSS	Fetal Intestine Large	intestine
28	chr10:94332800-94335000	Active TSS	K562	blood
29	chr10:94332800-94335200	Active TSS	Thymus	Thymus
30	chr10:94333000-94334800	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr10:94333000-94335000	Active TSS	Fetal Brain Female	brain
32	chr10:94333000-94335200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr10:94333200-94334800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:94333200-94335000	Active TSS	Primary T cells fromperipheralblood	blood
35	chr10:94334200-94335000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr10:94334200-94335000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr10:94334200-94335000	Flanking Active TSS	Dnd41	blood
38	chr10:94334400-94334800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr10:94334400-94334800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:94334400-94334800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr10:94334400-94334800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr10:94334400-94334800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr10:94334400-94334800	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr10:94334400-94334800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr10:94334400-94334800	Flanking Active TSS	Fetal Thymus	thymus
46	chr10:94334400-94334800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr10:94334400-94335000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:94334400-94335000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:94334400-94335000	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr10:94334400-94335000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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