Variant report

Variant	rs689980
Chromosome Location	chr9:98797911-98797912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1627425	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628930	0.85[EUR][1000 genomes]
rs2296857	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs238	0.83[AMR][1000 genomes]
rs686604	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690575	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7023522	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs689980	LINC00476	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
2	chr9:98793600-98800800	Weak transcription	Brain Substantia Nigra	brain
3	chr9:98793600-98804600	Weak transcription	Fetal Heart	heart
4	chr9:98794400-98801000	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:98794600-98799400	Weak transcription	Pancreas	Pancrea
6	chr9:98796400-98798200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:98796800-98802000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:98797000-98798000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:98797800-98798200	ZNF genes & repeats	Fetal Lung	lung

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Input of quick search could be:

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

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