Variant report

Variant	rs2793688
Chromosome Location	chr1:56766830-56766831
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2792783	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2792794	0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2792795	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793660	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793661	0.89[CHB][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793664	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2793672	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793675	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2793677	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793681	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793683	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793684	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793690	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9436538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9436999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947252	0.86[AMR][1000 genomes];0.81[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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2793688	HSPB11	cis	parietal	SCAN
rs2793688	TTC4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56757800-56786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:56758000-56768000	Weak transcription	Right Ventricle	heart
3	chr1:56758600-56770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:56759800-56767600	Weak transcription	Aorta	Aorta
5	chr1:56759800-56768000	Weak transcription	Left Ventricle	heart
6	chr1:56763600-56767600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:56763600-56767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:56763800-56768200	Weak transcription	Fetal Heart	heart
9	chr1:56763800-56770400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:56764000-56767200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:56764000-56767800	Weak transcription	Placenta	Placenta
12	chr1:56764000-56773400	Weak transcription	Psoas Muscle	Psoas
13	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:56765600-56769200	Weak transcription	Ovary	ovary
15	chr1:56765800-56775000	Weak transcription	HepG2	liver
16	chr1:56766200-56767800	Weak transcription	Fetal Intestine Large	intestine
17	chr1:56766200-56767800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:56766600-56769000	Enhancers	HUVEC	blood vessel
19	chr1:56766600-56770000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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