Variant report

Variant	rs4986825
Chromosome Location	chr3:51979120-51979121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51979065-51979155	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51976909..51979243-chr3:51994383..51996203,2	MCF-7	breast:
2	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
3	chr3:51976676..51979243-chr3:51995471..51997610,2	K562	blood:
4	chr3:51976311..51979172-chr3:51989239..51992217,2	K562	blood:
5	chr3:51978186..51980249-chr3:52021507..52023426,2	K562	blood:
6	chr3:51976078..51979243-chr3:51993727..51997610,4	K562	blood:
7	chr3:51976428..51980212-chr3:52001978..52006587,6	MCF-7	breast:
8	chr3:51978894..51981977-chr3:52001614..52003382,3	MCF-7	breast:
9	chr3:51977575..51979816-chr3:51980206..51981763,2	K562	blood:
10	chr3:51976344..51977998-chr3:51978167..51981813,4	MCF-7	breast:

No data

Variant related genes	Relation type
RRP9	TF binding region
PARP3	TF binding region
ENSG00000041880	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000248487	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];0.89[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876052	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188953	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2271069	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323864	0.86[ASN][1000 genomes]
rs323868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323881	0.89[ASN][1000 genomes]
rs323885	0.89[ASN][1000 genomes]
rs323886	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323893	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323894	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323895	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs56715917	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59682660	0.86[ASN][1000 genomes]
rs61546679	0.86[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51976800-51980600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:51977200-51982000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:51977200-51983000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:51977200-51987600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:51977200-51989200	Weak transcription	Ovary	ovary
6	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
7	chr3:51977400-51979400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:51977400-51981600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:51977400-51986200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:51977400-51987200	Weak transcription	Fetal Lung	lung
11	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
12	chr3:51977600-51979200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:51977600-51979200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:51977600-51979200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:51977600-51979800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:51977600-51981600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:51977600-51981600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:51977600-51982200	Weak transcription	NHLF	lung
19	chr3:51977600-51982400	Weak transcription	A549	lung
20	chr3:51977600-51982800	Weak transcription	GM12878-XiMat	blood
21	chr3:51977600-51983400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:51977600-51984400	Weak transcription	HepG2	liver
23	chr3:51977600-51986000	Weak transcription	Fetal Intestine Large	intestine
24	chr3:51977600-51987200	Weak transcription	HSMMtube	muscle
25	chr3:51977600-51987600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:51977600-51987600	Weak transcription	HSMM	muscle
27	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
29	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
30	chr3:51977800-51980400	Strong transcription	Right Ventricle	heart
31	chr3:51977800-51981600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:51977800-51983600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:51977800-51984000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:51977800-51985600	Weak transcription	Stomach Mucosa	stomach
35	chr3:51977800-51986000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:51977800-51987200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:51977800-51987800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:51978000-51982200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:51978200-51980400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:51978200-51980600	Strong transcription	Gastric	stomach
42	chr3:51978200-51980600	Strong transcription	Osteobl	bone
43	chr3:51978200-51982400	Strong transcription	Fetal Intestine Small	intestine
44	chr3:51978200-51983400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:51978200-51983600	Strong transcription	Fetal Stomach	stomach
46	chr3:51978200-51983600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:51978200-51983600	Strong transcription	Spleen	Spleen
48	chr3:51978200-51983800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:51978200-51984200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:51978400-51979600	Strong transcription	Fetal Muscle Leg	muscle

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