Variant report

Variant	rs2061721
Chromosome Location	chr20:52883857-52883858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52720871..52722915-chr20:52882468..52884514,2	MCF-7	breast:
2	chr20:52867284..52867978-chr20:52883331..52884092,2	MCF-7	breast:
3	chr20:52881988..52885819-chr20:52932723..52935221,3	MCF-7	breast:
4	chr20:52882962..52884659-chr20:53063631..53065695,2	MCF-7	breast:
5	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:
6	chr20:52824429..52825065-chr20:52883808..52884537,2	MCF-7	breast:
7	chr20:52823148..52829420-chr20:52882441..52888238,13	MCF-7	breast:
8	chr20:52883328..52886194-chr20:52903780..52906080,2	MCF-7	breast:
9	chr20:52883800..52885374-chr20:52939481..52942023,2	MCF-7	breast:
10	chr20:52209254..52210865-chr20:52881648..52883949,2	MCF-7	breast:
11	chr20:52882880..52885132-chr3:63848475..63850239,2	MCF-7	breast:
12	chr20:52881900..52884717-chr20:52925408..52927187,2	MCF-7	breast:
13	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
14	chr20:52846960..52850669-chr20:52882090..52885757,4	MCF-7	breast:
15	chr20:52855219..52857176-chr20:52882201..52884210,2	MCF-7	breast:
16	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
17	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
18	chr20:52882722..52884267-chr20:53265302..53267025,2	MCF-7	breast:
19	chr20:52872714..52873402-chr20:52883465..52884136,2	MCF-7	breast:
20	chr19:38794163..38796010-chr20:52883229..52885168,2	MCF-7	breast:
21	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:
22	chr20:52845835..52847665-chr20:52881455..52883980,2	MCF-7	breast:
23	chr20:52841965..52845171-chr20:52882309..52885405,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163635	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000163634	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1293132	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1298513	0.85[ASN][1000 genomes]
rs1382015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477729	0.90[AFR][1000 genomes]
rs1477730	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2616330	0.82[ASN][1000 genomes]
rs292120	0.84[ASN][1000 genomes]
rs292123	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs292125	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs292126	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs292132	0.87[ASN][1000 genomes]
rs292139	0.91[ASN][1000 genomes]
rs292141	0.90[ASN][1000 genomes]
rs292143	0.92[ASN][1000 genomes]
rs292144	0.87[ASN][1000 genomes]
rs292146	0.89[ASN][1000 genomes]
rs6013944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6023082	0.90[ASN][1000 genomes]
rs6091842	0.90[AFR][1000 genomes]
rs6097884	0.80[AFR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52874200-52884000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:52880600-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:52881000-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:52881200-52884000	Weak transcription	Fetal Lung	lung
5	chr20:52881200-52885000	Weak transcription	Fetal Stomach	stomach
6	chr20:52882800-52884200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:52883200-52885000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:52883400-52884400	Enhancers	Esophagus	oesophagus
9	chr20:52883400-52884800	Enhancers	HMEC	breast
10	chr20:52883400-52885200	Enhancers	Ovary	ovary
11	chr20:52883400-52885400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr20:52883400-52885600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr20:52883400-52885600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:52883400-52885600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:52883400-52885600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr20:52883400-52885800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:52883400-52885800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr20:52883400-52885800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr20:52883400-52885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:52883400-52885800	Enhancers	Placenta	Placenta
21	chr20:52883400-52886600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr20:52883600-52884000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:52883600-52884200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr20:52883600-52884200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:52883600-52884400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:52883600-52884400	Enhancers	Hela-S3	cervix
27	chr20:52883600-52884600	Bivalent Enhancer	HepG2	liver
28	chr20:52883600-52884800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:52883600-52884800	Enhancers	Stomach Mucosa	stomach
30	chr20:52883600-52885000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr20:52883600-52885400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr20:52883600-52886000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:52883600-52886000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr20:52883600-52886200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr20:52883600-52886200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr20:52883800-52884000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr20:52883800-52884400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:52883800-52884400	Enhancers	Pancreas	Pancrea
39	chr20:52883800-52884400	Enhancers	Osteobl	bone
40	chr20:52883800-52884600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr20:52883800-52884600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr20:52883800-52884600	Enhancers	Aorta	Aorta
43	chr20:52883800-52884600	Enhancers	NH-A	brain
44	chr20:52883800-52884600	Enhancers	NHEK	skin
45	chr20:52883800-52884800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:52883800-52884800	Enhancers	HSMMtube	muscle
47	chr20:52883800-52886000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr20:52883800-52886000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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