Variant report

Variant	rs10514330
Chromosome Location	chr5:89901848-89901849
allele	C/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	chr5:89900781..89902890-chr5:89944313..89947231,2	K562	blood:
2	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
3	chr5:89883022..89885296-chr5:89901095..89903175,2	K562	blood:
4	chr5:89704196..89707423-chr5:89899106..89902473,4	K562	blood:
5	chr5:89853355..89855789-chr5:89900091..89901923,2	MCF-7	breast:
6	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:
7	chr5:89824298..89826504-chr5:89901067..89902762,2	MCF-7	breast:
8	chr5:89767614..89772956-chr5:89898929..89905987,8	K562	blood:
9	chr5:89900245..89902488-chr5:89903253..89905685,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10056775	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11738461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738532	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11739958	0.81[EUR][1000 genomes]
rs11742844	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11745908	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11748911	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11749693	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13153138	0.84[EUR][1000 genomes]
rs13157270	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs13159048	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13164404	0.91[EUR][1000 genomes]
rs13167847	1.00[AFR][1000 genomes]
rs13171056	0.81[EUR][1000 genomes]
rs13182944	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13183331	0.81[EUR][1000 genomes]
rs13186124	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13189520	0.80[CEU][hapmap]
rs13190272	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1508788	0.80[CEU][hapmap]
rs16868809	0.86[AFR][1000 genomes]
rs17541517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17541704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17541912	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17542086	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17542921	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17543150	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17552645	1.00[CEU][hapmap]
rs17614588	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17621038	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17621160	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17621985	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17622555	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28399862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28429067	0.86[AFR][1000 genomes]
rs34301936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34490215	0.86[EUR][1000 genomes]
rs34719862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34774423	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35312877	0.81[EUR][1000 genomes]
rs35667071	0.91[EUR][1000 genomes]
rs35680172	0.81[EUR][1000 genomes]
rs35683645	0.81[EUR][1000 genomes]
rs35980777	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36045161	0.81[EUR][1000 genomes]
rs6452887	1.00[CEU][hapmap]
rs66683260	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6877613	1.00[CEU][hapmap]
rs71637308	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89892800-89909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:89893000-89907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:89893200-89902000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:89895000-89907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89899600-89902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:89900400-89903200	Enhancers	K562	blood
7	chr5:89900800-89902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:89901000-89908200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links