Variant report

Variant	rs6550956
Chromosome Location	chr3:25214024-25214025
allele	A/T
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	POLR2A	chr3:25213921-25214064	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr3:25212226-25214085	SK-N-SH	brain:	n/a	chr3:25213135-25213149 chr3:25213137-25213151 chr3:25213138-25213152 chr3:25213452-25213462 chr3:25213136-25213150 chr3:25212704-25212714

Variant related genes	Relation type
RARB	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10865803	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11129189	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11711099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711519	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11711829	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491526	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495130	0.86[EUR][1000 genomes]
rs12638845	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067015	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13092408	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093241	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1347559	0.84[ASN][1000 genomes]
rs1369873	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369874	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436236	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436237	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436238	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1603980	0.82[EUR][1000 genomes]
rs1603982	0.85[EUR][1000 genomes]
rs1836840	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2196466	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681040	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858144	0.80[ASN][1000 genomes]
rs62228592	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6788715	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796800	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623185	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7639228	0.87[ASN][1000 genomes]
rs7640571	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645872	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs767823	0.81[ASN][1000 genomes]
rs904592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs931696	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs931697	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][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	nsv1013446	chr3:25176609-25221334	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876631	chr3:25185448-25231571	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv949035	chr3:25194301-26084890	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv508213	chr3:25206150-25326196	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25200600-25214600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:25208000-25215200	Weak transcription	Fetal Lung	lung
3	chr3:25211800-25216800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:25212000-25215800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:25212400-25215800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:25212600-25215600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:25212800-25216400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:25213000-25215600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:25213600-25215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:25213600-25218800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:25213800-25214800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:25213800-25215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:25214000-25218000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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