Variant report

Variant	rs535453
Chromosome Location	chr9:104182490-104182491
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:104159430..104161910-chr9:104180368..104183208,3	MCF-7	breast:
2	chr9:104167280..104171241-chr9:104178855..104183117,5	K562	blood:
3	chr9:104167820..104171241-chr9:104178855..104183117,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF189-2	chr9:104181299-104185086	NONHSAT133730

Variant related genes	Relation type
ENSG00000136897	Chromatin interaction
ENSG00000136870	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1233983	0.99[ASN][1000 genomes]
rs2777342	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2777345	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2777347	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777348	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2777349	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535787	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs475348	0.99[ASN][1000 genomes]
rs476046	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480792	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs491979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs504023	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs525998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs546577	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs578597	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs578770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852444	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104172800-104187000	Weak transcription	Left Ventricle	heart
2	chr9:104176400-104185600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:104178000-104182600	Weak transcription	Liver	Liver
4	chr9:104178200-104186800	Weak transcription	Fetal Brain Female	brain
5	chr9:104178400-104183600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:104178400-104187000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:104179400-104188800	Enhancers	HepG2	liver
8	chr9:104179800-104182800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:104180400-104184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:104180600-104185800	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:104181200-104183600	Weak transcription	Aorta	Aorta
12	chr9:104181200-104184000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:104181800-104183800	Weak transcription	Fetal Intestine Small	intestine
14	chr9:104181800-104184000	Weak transcription	Pancreas	Pancrea
15	chr9:104181800-104184200	Weak transcription	HSMMtube	muscle
16	chr9:104181800-104187600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:104182400-104183600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:104182400-104189600	Weak transcription	Ovary	ovary

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