Variant report

Variant	rs6890575
Chromosome Location	chr5:89867823-89867824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
2	chr5:89853120..89856686-chr5:89866330..89870459,4	MCF-7	breast:
3	chr5:89856963..89860302-chr5:89865083..89868215,3	MCF-7	breast:
4	chr5:89851829..89860351-chr5:89861712..89870170,13	K562	blood:
5	chr5:89862796..89864795-chr5:89866978..89869006,2	K562	blood:
6	chr5:89705110..89707886-chr5:89867244..89868885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10061554	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10063133	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10068222	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069574	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109357	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332360	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332567	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332756	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332758	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995555	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2886763	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59103759	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6452891	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6452893	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6452894	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6897313	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73176018	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73176092	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73177814	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73177822	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7706392	1.00[EUR][1000 genomes]
rs7709218	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724959	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7726094	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7736668	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7737581	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	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
4	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
5	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
6	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
7	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
8	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89855200-89871000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:89859400-89884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:89860200-89868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:89865800-89869200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:89866800-89868600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:89866800-89868800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:89866800-89868800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:89867000-89868800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:89867400-89868600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:89867400-89869000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:89867400-89872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:89867400-89889200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:89867600-89868400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:89867800-89871400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links