Variant report

Variant	rs793039
Chromosome Location	chr20:52956100-52956101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52947709..52951079-chr20:52955408..52958637,4	MCF-7	breast:
2	chr20:52926101..52927623-chr20:52956080..52958145,2	MCF-7	breast:
3	chr20:52955260..52957425-chr20:52959176..52960946,2	K562	blood:
4	chr20:52955311..52960636-chr20:52963948..52966775,4	MCF-7	breast:
5	chr20:52823411..52827857-chr20:52956007..52962022,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1087050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1293147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1477739	1.00[EUR][1000 genomes]
rs16999399	1.00[EUR][1000 genomes]
rs16999732	1.00[EUR][1000 genomes]
rs2219732	1.00[EUR][1000 genomes]
rs2426520	1.00[EUR][1000 genomes]
rs2426521	1.00[EUR][1000 genomes]
rs2616329	1.00[EUR][1000 genomes]
rs2616331	1.00[EUR][1000 genomes]
rs2616334	1.00[EUR][1000 genomes]
rs2616337	1.00[EUR][1000 genomes]
rs2797969	1.00[EUR][1000 genomes]
rs55972874	1.00[EUR][1000 genomes]
rs56977264	1.00[EUR][1000 genomes]
rs57927391	1.00[EUR][1000 genomes]
rs6013977	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6013981	1.00[ASN][1000 genomes]
rs6014025	1.00[EUR][1000 genomes]
rs60215168	1.00[EUR][1000 genomes]
rs6023260	1.00[EUR][1000 genomes]
rs6023271	1.00[EUR][1000 genomes]
rs6091884	1.00[EUR][1000 genomes]
rs6091909	1.00[EUR][1000 genomes]
rs6097927	0.94[ASN][1000 genomes]
rs6097991	1.00[EUR][1000 genomes]
rs6097995	1.00[EUR][1000 genomes]
rs61495423	1.00[EUR][1000 genomes]
rs62214388	1.00[EUR][1000 genomes]
rs707552	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7264904	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs793040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs793045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793047	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs793048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs793049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs811571	1.00[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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52951000-52957200	Weak transcription	Gastric	stomach
2	chr20:52952400-52956600	Weak transcription	Osteobl	bone
3	chr20:52952400-52956800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52952400-52956800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr20:52955600-52956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:52955800-52957000	Enhancers	NH-A	brain
7	chr20:52956000-52956200	Flanking Active TSS	HUVEC	blood vessel
8	chr20:52956000-52963800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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