Variant report

Variant	rs11715208
Chromosome Location	chr3:52309827-52309828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52266609..52268371-chr3:52308578..52311025,2	MCF-7	breast:
2	chr3:52264055..52267306-chr3:52309351..52312799,8	MCF-7	breast:
3	chr3:52282752..52284466-chr3:52308122..52311758,3	K562	blood:
4	chr3:52306677..52308249-chr3:52309532..52311705,2	MCF-7	breast:
5	chr3:52279829..52282973-chr3:52309699..52312689,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173366	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	0.97[EUR][1000 genomes]
rs10461027	0.97[EUR][1000 genomes]
rs10461028	0.91[EUR][1000 genomes]
rs10865971	0.83[EUR][1000 genomes]
rs11706515	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706541	0.93[EUR][1000 genomes]
rs11707056	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708581	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11710014	0.97[EUR][1000 genomes]
rs11711914	0.94[EUR][1000 genomes]
rs11711974	0.94[EUR][1000 genomes]
rs11713914	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714358	1.00[EUR][1000 genomes]
rs11715382	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715391	0.97[EUR][1000 genomes]
rs11717028	0.97[EUR][1000 genomes]
rs11718729	0.96[EUR][1000 genomes]
rs11719760	0.93[EUR][1000 genomes]
rs11720365	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11721277	0.94[EUR][1000 genomes]
rs17052051	0.96[EUR][1000 genomes]
rs17052052	0.98[EUR][1000 genomes]
rs17052053	0.96[EUR][1000 genomes]
rs17052054	1.00[EUR][1000 genomes]
rs17263770	0.81[EUR][1000 genomes]
rs1767	0.96[EUR][1000 genomes]
rs1769	1.00[EUR][1000 genomes]
rs35976326	1.00[EUR][1000 genomes]
rs3733063	0.96[EUR][1000 genomes]
rs3886875	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4082828	0.96[EUR][1000 genomes]
rs55676974	1.00[EUR][1000 genomes]
rs55806905	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55813842	0.94[EUR][1000 genomes]
rs55847657	0.96[EUR][1000 genomes]
rs56002041	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.94[EUR][1000 genomes]
rs56352611	0.96[EUR][1000 genomes]
rs56899118	0.94[EUR][1000 genomes]
rs57849650	0.94[EUR][1000 genomes]
rs58531656	0.96[EUR][1000 genomes]
rs60382084	0.96[EUR][1000 genomes]
rs61644644	1.00[EUR][1000 genomes]
rs6445385	0.96[EUR][1000 genomes]
rs67767125	0.86[AMR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	1.00[EUR][1000 genomes]
rs6793317	0.96[EUR][1000 genomes]
rs6809248	0.96[EUR][1000 genomes]
rs724801	0.82[EUR][1000 genomes]
rs729555	0.82[EUR][1000 genomes]
rs73072990	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73088773	0.97[EUR][1000 genomes]
rs73088783	0.96[EUR][1000 genomes]
rs73088785	0.96[EUR][1000 genomes]
rs73088791	1.00[EUR][1000 genomes]
rs73088800	0.96[EUR][1000 genomes]
rs73091166	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73091168	0.94[EUR][1000 genomes]
rs746239	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615405	0.97[EUR][1000 genomes]
rs7628461	0.96[EUR][1000 genomes]
rs7633687	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638204	0.97[EUR][1000 genomes]
rs7643913	1.00[EUR][1000 genomes]

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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:52297400-52311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52300000-52310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:52300000-52310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52300200-52310200	Weak transcription	HSMMtube	muscle
6	chr3:52300600-52310800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52301200-52311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:52302600-52310000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:52302800-52310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:52303000-52311200	Weak transcription	Esophagus	oesophagus
11	chr3:52303400-52310000	Weak transcription	Aorta	Aorta
12	chr3:52304000-52311000	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr3:52304400-52310200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:52305000-52310000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52305000-52310400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:52305200-52310400	Genic enhancers	Fetal Thymus	thymus
17	chr3:52305600-52310000	Genic enhancers	HepG2	liver
18	chr3:52305800-52310200	Genic enhancers	Fetal Muscle Leg	muscle
19	chr3:52305800-52310200	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr3:52306000-52310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:52306600-52310800	Weak transcription	Lung	lung
22	chr3:52307000-52310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:52307000-52311600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr3:52307200-52310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:52307200-52310000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:52307200-52310200	Weak transcription	Colonic Mucosa	Colon
27	chr3:52307400-52310200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:52307400-52310200	Enhancers	Liver	Liver
29	chr3:52307600-52310200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52307600-52311200	Enhancers	Placenta	Placenta
31	chr3:52308000-52310000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:52308000-52310400	Enhancers	Stomach Mucosa	stomach
33	chr3:52308000-52310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:52308200-52310000	Enhancers	Fetal Heart	heart
35	chr3:52308200-52310400	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:52308200-52311000	Enhancers	Spleen	Spleen
37	chr3:52308400-52310000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:52308400-52310000	Strong transcription	Fetal Intestine Small	intestine
39	chr3:52308400-52310000	Enhancers	Ovary	ovary
40	chr3:52308400-52310400	Enhancers	Brain Substantia Nigra	brain
41	chr3:52308400-52311200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:52308600-52310000	Genic enhancers	K562	blood
43	chr3:52308600-52310000	Weak transcription	NH-A	brain
44	chr3:52308600-52310600	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:52308800-52310200	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr3:52309000-52310000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:52309000-52310000	Strong transcription	Fetal Stomach	stomach
48	chr3:52309000-52310600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:52309000-52310800	Weak transcription	Pancreas	Pancrea
50	chr3:52309200-52310200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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