Variant report

Variant	rs7781924
Chromosome Location	chr7:50907307-50907308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50906192..50908348-chr7:50915043..50917108,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRB10-1	chr7:50907060-50907362	ENSG00000236046

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10226465	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230084	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233389	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs10234720	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10242300	0.85[EUR][1000 genomes]
rs10250894	0.85[EUR][1000 genomes]
rs10264737	0.81[CEU][hapmap]
rs10267953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282345	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718959	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12718961	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17454517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17564264	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862946	0.85[EUR][1000 genomes]
rs1862948	0.85[EUR][1000 genomes]
rs4947934	0.83[ASN][1000 genomes]
rs4947936	0.87[EUR][1000 genomes]
rs4947937	0.86[EUR][1000 genomes]
rs4947938	0.86[EUR][1000 genomes]
rs4947939	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947945	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6976298	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7350021	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357209	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802799	0.86[EUR][1000 genomes]
rs9656704	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv606907	chr7:50899168-51195380	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7781924	VWC2	cis	cerebellum	SCAN
rs7781924	SEC61G	cis	parietal	SCAN
rs7781924	ABCA13	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50904800-50907400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr7:50904800-50907800	Enhancers	HUVEC	blood vessel
3	chr7:50905000-50907800	Enhancers	Osteobl	bone
4	chr7:50905200-50907400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:50905200-50907600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:50905600-50907400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:50905600-50907400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:50906000-50907400	Enhancers	NHDF-Ad	bronchial
9	chr7:50906000-50907600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:50906000-50907800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr7:50906000-50908000	Enhancers	A549	lung
12	chr7:50906000-50908000	Enhancers	Hela-S3	cervix
13	chr7:50906200-50907400	Enhancers	HSMM	muscle
14	chr7:50906400-50907600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr7:50906800-50907800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:50907000-50907400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:50907000-50907400	Enhancers	Adipose Nuclei	Adipose
18	chr7:50907200-50907400	Enhancers	NH-A	brain
19	chr7:50907200-50916800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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