Variant report

Variant	rs9850781
Chromosome Location	chr3:24587580-24587581
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24534792..24536707-chr3:24586895..24591064,3	K562	blood:
2	chr3:24561877..24564685-chr3:24585001..24587984,3	K562	blood:
3	chr3:24563185..24564896-chr3:24586484..24588890,2	K562	blood:
4	chr3:24578631..24583271-chr3:24586680..24589577,4	K562	blood:
5	chr3:24535527..24537870-chr3:24586121..24588310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265028	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10212332	0.84[ASN][1000 genomes]
rs10490837	0.84[EUR][1000 genomes]
rs11708042	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712286	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13318800	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561079	0.81[ASN][1000 genomes]
rs17014900	0.86[EUR][1000 genomes]
rs17014902	0.86[EUR][1000 genomes]
rs17029611	0.81[ASN][1000 genomes]
rs1992040	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992041	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2117873	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117874	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2196434	0.85[ASN][1000 genomes]
rs2196438	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562279	0.82[EUR][1000 genomes]
rs56268655	0.87[EUR][1000 genomes]
rs58152527	0.86[ASN][1000 genomes]
rs61701305	0.86[ASN][1000 genomes]
rs6550878	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6550879	0.86[ASN][1000 genomes]
rs6767534	0.96[ASN][1000 genomes]
rs6767717	0.85[ASN][1000 genomes]
rs6769209	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770518	0.86[ASN][1000 genomes]
rs6771818	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781066	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6795607	0.81[ASN][1000 genomes]
rs6801494	0.85[ASN][1000 genomes]
rs73038411	0.87[EUR][1000 genomes]
rs73038427	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73040438	0.85[EUR][1000 genomes]
rs73040440	0.81[EUR][1000 genomes]
rs7647700	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930317	0.85[ASN][1000 genomes]
rs9310745	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819865	0.85[ASN][1000 genomes]
rs9823545	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830859	0.90[ASN][1000 genomes]
rs9835497	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838720	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844544	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9853927	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859978	0.85[ASN][1000 genomes]
rs9861129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868375	0.90[ASN][1000 genomes]
rs9873830	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878606	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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24566200-24591800	Weak transcription	Psoas Muscle	Psoas
2	chr3:24582600-24588400	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:24586200-24588200	Enhancers	Fetal Lung	lung
4	chr3:24587000-24587800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:24587000-24588000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:24587000-24590400	Enhancers	Liver	Liver
7	chr3:24587200-24587600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:24587200-24587800	Enhancers	Hela-S3	cervix
9	chr3:24587200-24588000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:24587200-24588000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:24587200-24588000	Enhancers	HepG2	liver
12	chr3:24587200-24588200	Enhancers	Adipose Nuclei	Adipose
13	chr3:24587200-24588800	Enhancers	NHDF-Ad	bronchial
14	chr3:24587200-24589600	Enhancers	HSMMtube	muscle
15	chr3:24587200-24590600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:24587400-24588200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links