Variant report

Variant	rs2235953
Chromosome Location	chr20:23019724-23019725
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:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23015312..23016906-chr20:23019292..23021304,2	MCF-7	breast:
2	chr20:23017212..23020123-chr20:23028174..23031939,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSTR4-1	chr20:23019571-23019873	ENSG00000234646.1
2	lnc-SSTR4-1	chr20:23019693-23019873	ENSG00000234646.1
3	lnc-SSTR4-1	chr20:23019693-23019865	NONHSAT079026
4	lnc-SSTR4-1	chr20:23019186-23019873	NONHSAT079025

No data

No data

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2092634	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2092635	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2092636	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2103760	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220987	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs220988	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220989	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424502	0.88[CHB][hapmap]
rs2567607	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2746620	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2746621	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57804096	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv524981	chr20:23011468-23021597	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23016000-23026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:23016200-23020600	Weak transcription	Right Atrium	heart
3	chr20:23016200-23028200	Weak transcription	Aorta	Aorta
4	chr20:23016600-23023600	Weak transcription	Gastric	stomach
5	chr20:23017600-23024600	Weak transcription	Spleen	Spleen
6	chr20:23017800-23020800	Weak transcription	Esophagus	oesophagus
7	chr20:23019200-23020000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr20:23019200-23020200	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr20:23019400-23020000	Enhancers	Fetal Heart	heart
10	chr20:23019400-23021000	Enhancers	HSMMtube	muscle
11	chr20:23019400-23021600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:23019600-23020800	Enhancers	HSMM	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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