Variant report

Variant	rs980876
Chromosome Location	chr9:26674986-26674987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10733410	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10738754	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10757621	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10757622	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12685912	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1347336	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1347337	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1541955	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1541956	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7047376	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7468773	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7871815	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs892567	0.85[EUR][1000 genomes]

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	nsv995049	chr9:26162115-26760535	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892854	chr9:26326100-26749094	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv892858	chr9:26609613-26783463	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv466330	chr9:26641557-26691668	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	lncRNA	n/a	inside rSNPs	diseases
5	nsv613939	chr9:26641557-26691668	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
6	nsv466331	chr9:26643035-26689442	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	lncRNA	n/a	inside rSNPs	diseases
7	nsv613940	chr9:26643035-26689442	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
8	nsv892859	chr9:26643035-26691668	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs980876	LINGO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26668000-26678400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:26670400-26681400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:26671200-26677600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:26673400-26677200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:26673800-26677400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:26674000-26675200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:26674400-26677400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:26674800-26675200	Enhancers	Hela-S3	cervix
9	chr9:26674800-26675600	Enhancers	NH-A	brain

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

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