Variant report

Variant	rs793050
Chromosome Location	chr20:52958016-52958017
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52892973..52894968-chr20:52956980..52958556,2	MCF-7	breast:
2	chr20:52947709..52951079-chr20:52955408..52958637,4	MCF-7	breast:
3	chr20:52926101..52927623-chr20:52956080..52958145,2	MCF-7	breast:
4	chr20:52861825..52864272-chr20:52956863..52959337,2	MCF-7	breast:
5	chr20:52955311..52960636-chr20:52963948..52966775,4	MCF-7	breast:
6	chr12:50536506..50537503-chr20:52957817..52958407,2	MCF-7	breast:
7	chr20:52823411..52827857-chr20:52956007..52962022,9	MCF-7	breast:
8	chr20:52956264..52958704-chr20:53136561..53138207,2	MCF-7	breast:
9	chr20:52957064..52959136-chr20:53012315..53013962,2	MCF-7	breast:
10	chr12:753066..755991-chr20:52956460..52959168,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1087050	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1293147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013977	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6013981	0.97[ASN][1000 genomes]
rs6097927	0.90[ASN][1000 genomes]
rs707552	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7264904	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793039	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs793045	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs793046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs793047	0.97[ASN][1000 genomes]
rs793048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811571	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52956000-52963800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52956600-52958400	Enhancers	Osteobl	bone
3	chr20:52956600-52958600	Enhancers	Hela-S3	cervix
4	chr20:52956800-52958200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr20:52957200-52958400	Enhancers	NHDF-Ad	bronchial
6	chr20:52957400-52961400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:52957600-52958400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:52957600-52959200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:52957600-52959200	Weak transcription	Fetal Brain Female	brain
10	chr20:52957600-52962000	Weak transcription	Colon Smooth Muscle	Colon
11	chr20:52957800-52958200	Enhancers	NH-A	brain
12	chr20:52957800-52958600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52957800-52958800	Weak transcription	Brain Germinal Matrix	brain
14	chr20:52957800-52960200	Weak transcription	A549	lung
15	chr20:52957800-52960800	Enhancers	HUVEC	blood vessel
16	chr20:52958000-52958200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr20:52958000-52959800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:52958000-52961200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:52958000-52961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52958000-52961400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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