Variant report

Variant	rs6880570
Chromosome Location	chr5:90001368-90001369
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:89992042..89994832-chr5:90000512..90002853,2	K562	blood:
2	chr5:89989350..89991740-chr5:90000493..90002123,2	K562	blood:
3	chr5:89989350..89991740-chr5:89999562..90002123,3	K562	blood:
4	chr5:89998991..90003482-chr5:90003758..90009177,7	K562	blood:
5	chr5:89996062..89998352-chr5:90001342..90003176,2	K562	blood:
6	chr5:89704471..89707067-chr5:89999894..90001997,2	K562	blood:
7	chr5:90001172..90003183-chr5:90006013..90008402,2	K562	blood:
8	chr5:89996062..89999170-chr5:90000730..90003176,4	K562	blood:
9	chr5:89992042..89994832-chr5:90000512..90002853,3	K562	blood:

No data

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

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10514331	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11951632	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs11952742	0.86[TSI][hapmap]
rs11955565	0.85[ASN][1000 genomes]
rs11959270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960887	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1344030	0.86[TSI][hapmap]
rs16868901	0.82[TSI][hapmap]
rs16868906	0.91[EUR][1000 genomes]
rs16868917	0.88[CEU][hapmap]
rs16868924	0.91[EUR][1000 genomes]
rs16868927	0.91[EUR][1000 genomes]
rs16868932	0.91[EUR][1000 genomes]
rs16868964	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16868970	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16868972	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16868985	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16869013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869032	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16869043	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1878881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366776	0.83[TSI][hapmap]
rs41303352	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41308295	0.91[EUR][1000 genomes]
rs4916809	0.88[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4916810	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs55720814	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58582125	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60562826	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61525440	0.80[EUR][1000 genomes]
rs6867004	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875517	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72656677	0.91[EUR][1000 genomes]
rs73772469	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707357	0.86[TSI][hapmap]
rs7709691	0.82[TSI][hapmap]
rs7721027	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7729205	0.81[EUR][1000 genomes]
rs7729644	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9293546	0.82[TSI][hapmap]
rs950692	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv882368	chr5:89990324-90012379	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1031718	chr5:89999033-90099868	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:89979200-90002600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:89982000-90004600	Weak transcription	Fetal Brain Female	brain
4	chr5:89987800-90007200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:89991800-90014000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:89994600-90001600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:89995000-90001600	Weak transcription	Brain Germinal Matrix	brain
8	chr5:89995000-90025800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:89997800-90017600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:89998800-90018000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:89999200-90002200	Strong transcription	K562	blood
12	chr5:89999600-90010000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:89999800-90004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:90001000-90001800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:90001200-90002000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:90001200-90002200	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:90001200-90002400	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links