Variant report

Variant	rs2562523
Chromosome Location	chr5:89830529-89830530
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89769294..89771048-chr5:89829508..89832155,2	MCF-7	breast:
2	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
3	chr5:89829518..89831624-chr5:89838668..89840450,2	K562	blood:
4	chr5:89829601..89833585-chr5:89854929..89859978,5	MCF-7	breast:
5	chr5:89828910..89830955-chr5:89855867..89858552,2	MCF-7	breast:
6	chr5:89827458..89830641-chr5:89851988..89854819,3	MCF-7	breast:
7	chr5:89824654..89827598-chr5:89828369..89833726,5	K562	blood:
8	chr5:89718278..89720087-chr5:89828600..89831257,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs154571	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs2247158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366768	0.85[CHB][hapmap]
rs2562515	0.85[CHB][hapmap]
rs257855	0.81[EUR][1000 genomes]
rs27202	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27601	0.83[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27602	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27657	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27658	0.85[CHB][hapmap]
rs37480	0.83[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37482	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40205	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7722900	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7726781	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89826200-89842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:89826600-89831000	Weak transcription	Fetal Intestine Small	intestine
3	chr5:89826600-89831200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:89826600-89833000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:89826600-89833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:89826800-89843200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:89827600-89831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:89829200-89833400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:89830400-89833400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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