Variant report

Variant	rs2070914
Chromosome Location	chr3:52487894-52487895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52487771-52488414	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr3:52487839-52488695	ECC-1	luminal epithelium:	n/a	n/a
3	HEY1	chr3:52487867-52488442	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52487865-52488335	HepG2	liver:	n/a	n/a
5	TEAD4	chr3:52487863-52488298	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr3:52487892-52488329	H1-hESC	embryonic stem cell:	n/a	n/a
7	NFIC	chr3:52487889-52488773	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr3:52487842-52488352	ECC-1	luminal epithelium:	n/a	n/a
9	RCOR1	chr3:52487554-52487953	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:52487850-52488105	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52487795-52488403	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:52487592-52491009	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
2	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:
3	chr3:52447983..52449593-chr3:52487471..52490265,2	K562	blood:

No data

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000010318	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2240897	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs758800	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
2	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:52481400-52488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:52483800-52489000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52483800-52489200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:52484000-52488000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
7	chr3:52484600-52488400	Weak transcription	NHEK	skin
8	chr3:52484600-52488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52484600-52489200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:52484800-52489000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52484800-52489000	Weak transcription	NH-A	brain
12	chr3:52485000-52488000	Active TSS	Right Atrium	heart
13	chr3:52485000-52488200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:52485000-52488600	Weak transcription	Liver	Liver
15	chr3:52485000-52488600	Weak transcription	HMEC	breast
16	chr3:52485200-52489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52485400-52489000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52485600-52489400	Flanking Active TSS	HepG2	liver
19	chr3:52486200-52488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:52486200-52489200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:52486400-52488200	Active TSS	Right Ventricle	heart
22	chr3:52486400-52488400	Active TSS	Left Ventricle	heart
23	chr3:52486400-52488800	Weak transcription	Fetal Brain Female	brain
24	chr3:52486600-52488000	Flanking Active TSS	HSMM	muscle
25	chr3:52486600-52488600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:52486600-52489000	Enhancers	Fetal Intestine Small	intestine
27	chr3:52486600-52489200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:52486600-52489200	Enhancers	Gastric	stomach
29	chr3:52486800-52488200	Active TSS	HSMMtube	muscle
30	chr3:52486800-52488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:52486800-52488800	Enhancers	Fetal Intestine Large	intestine
32	chr3:52486800-52489000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:52486800-52489000	Enhancers	A549	lung
34	chr3:52487000-52488000	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr3:52487000-52488600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:52487000-52488600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr3:52487200-52488000	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr3:52487200-52488200	Weak transcription	Stomach Mucosa	stomach
39	chr3:52487200-52488600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:52487200-52488600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:52487200-52488600	Enhancers	GM12878-XiMat	blood
42	chr3:52487200-52488800	Enhancers	Esophagus	oesophagus
43	chr3:52487200-52489000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:52487200-52489000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:52487200-52489000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:52487200-52489000	Enhancers	Fetal Lung	lung
47	chr3:52487200-52489400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:52487400-52488000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:52487400-52488000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:52487400-52488000	Flanking Active TSS	Hela-S3	cervix

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