Variant report

Variant	rs62217199
Chromosome Location	chr20:25061530-25061531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr20:25061484-25062220	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
2	REST	chr20:25061158-25062456	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
3	REST	chr20:25061399-25062180	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
4	REST	chr20:25061317-25062186	PFSK-1	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
5	REST	chr20:25061458-25062106	HCT-116	colon:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
6	REST	chr20:25061341-25062199	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
7	REST	chr20:25061527-25061998	U87	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
8	REST	chr20:25061492-25062187	SK-N-SH	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
9	REST	chr20:25061294-25062307	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
10	REST	chr20:25061128-25062227	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
11	REST	chr20:25061395-25062174	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
12	REST	chr20:25061376-25062443	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
13	REST	chr20:25061267-25062399	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
14	REST	chr20:25061397-25062115	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
15	REST	chr20:25061353-25062229	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
16	REST	chr20:25061483-25062126	GM12878	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
17	REST	chr20:25061290-25062145	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
18	REST	chr20:25061411-25062291	HL-60	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
19	REST	chr20:25061306-25062231	PFSK-1	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
20	TEAD4	chr20:25061509-25062136	A549	lung:	n/a	n/a
21	REST	chr20:25061036-25062526	HL-60	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25054332..25057280-chr20:25059401..25062693,3	K562	blood:

Variant related genes	Relation type
VSX1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1005409	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13036777	0.83[AFR][1000 genomes]
rs2207632	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	1.00[ASN][1000 genomes]
rs4813546	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	1.00[ASN][1000 genomes]
rs4815366	1.00[ASN][1000 genomes]
rs4815367	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	1.00[ASN][1000 genomes]
rs6083736	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217194	0.82[EUR][1000 genomes]
rs62217195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7266451	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7344824	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25058800-25061800	Weak transcription	Pancreas	Pancrea
2	chr20:25060600-25062600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links