Variant report

Variant	rs10490227
Chromosome Location	chr2:50659515-50659516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11125305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11885804	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11901106	0.84[ASN][1000 genomes]
rs17040648	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915170	0.83[MEX][hapmap]
rs4563262	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs4971677	0.91[EUR][1000 genomes]
rs4971678	1.00[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6756081	0.81[JPT][hapmap]
rs719293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72878310	0.83[ASN][1000 genomes]
rs73934105	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599052	0.83[MEX][hapmap]
rs989378	0.91[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs9917153	0.82[CHB][hapmap];0.90[JPT][hapmap]

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	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50659000-50660000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:50659000-50660200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:50659000-50660200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr2:50659000-50660400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:50659000-50660400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:50659000-50660400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:50659200-50660800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:50659400-50659800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:50659400-50660000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:50659400-50660000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:50659400-50660200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:50659400-50660200	Enhancers	Brain Germinal Matrix	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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