Variant report

Variant	rs7357209
Chromosome Location	chr7:50906903-50906904
allele	G/T
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:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10226465	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230084	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233389	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10234720	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1023633	0.81[CEU][hapmap]
rs10242300	0.94[EUR][1000 genomes]
rs10250894	0.94[EUR][1000 genomes]
rs10267953	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718959	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12718961	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17454517	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17564264	1.00[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]
rs1862946	0.94[EUR][1000 genomes]
rs1862948	0.94[EUR][1000 genomes]
rs2161825	0.81[CEU][hapmap]
rs4947477	0.83[EUR][1000 genomes]
rs4947478	0.84[EUR][1000 genomes]
rs4947934	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947936	0.96[EUR][1000 genomes]
rs4947937	0.95[EUR][1000 genomes]
rs4947938	0.95[EUR][1000 genomes]
rs4947939	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947945	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6593252	0.81[CEU][hapmap]
rs6976298	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7350021	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779063	0.81[CEU][hapmap]
rs7781924	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802799	0.95[EUR][1000 genomes]
rs9656704	0.95[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
rs7357209	ALS2CR4	trans	brain	seeQTL
rs7357209	VWC2	cis	cerebellum	SCAN
rs7357209	CCDC28A	trans	brain	seeQTL

Chromatin state (count:26 , 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	chr7:50905200-50907000	Enhancers	Fetal Lung	lung
5	chr7:50905200-50907400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:50905200-50907600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:50905600-50907000	Bivalent Enhancer	HepG2	liver
8	chr7:50905600-50907200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:50905600-50907200	Enhancers	NHLF	lung
10	chr7:50905600-50907400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:50905600-50907400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:50906000-50907000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:50906000-50907200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:50906000-50907200	Enhancers	HSMMtube	muscle
15	chr7:50906000-50907400	Enhancers	NHDF-Ad	bronchial
16	chr7:50906000-50907600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:50906000-50907800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:50906000-50908000	Enhancers	A549	lung
19	chr7:50906000-50908000	Enhancers	Hela-S3	cervix
20	chr7:50906200-50907000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:50906200-50907400	Enhancers	HSMM	muscle
22	chr7:50906400-50907000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:50906400-50907600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr7:50906600-50907000	Enhancers	NH-A	brain
25	chr7:50906800-50907200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr7:50906800-50907800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links