Variant report

Variant	rs62559007
Chromosome Location	chr9:98553263-98553264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1369156	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1836404	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72756397	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62559007	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs62559007	LINC00476	cis	Adipose Subcutaneous	GTEx
rs62559007	LINC00476	cis	Artery Aorta	GTEx
rs62559007	LINC00476	cis	Esophagus Mucosa	GTEx
rs62559007	LINC00476	cis	lung	GTEx
rs62559007	LINC00476	cis	Thyroid	GTEx
rs62559007	LINC00476	cis	Stomach	GTEx
rs62559007	LINC00476	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548200-98553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:98548200-98558400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:98551000-98553400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:98551000-98553600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:98551200-98553600	Weak transcription	HepG2	liver
7	chr9:98553000-98555800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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