Variant report

Variant	rs784852
Chromosome Location	chr12:119895875-119895876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1358351	0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1716466	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs516016	0.97[GIH][hapmap];0.80[MEX][hapmap]
rs7312027	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs739424	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs784842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs804401	0.84[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884033	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047036	chr12:119477583-119992640	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv916688	chr12:119801814-120044407	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832529	chr12:119863378-120071646	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs784852	VSIG10	cis	cerebellum	SCAN
rs784852	TESC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:119894600-119897400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:119894800-119896000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:119894800-119896000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr12:119894800-119896200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:119895000-119896000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:119895000-119896000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:119895200-119896000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:119895400-119896000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr12:119895600-119896200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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