Variant report

Variant	rs2519739
Chromosome Location	chr7:18812445-18812446
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10215908	1.00[JPT][hapmap]
rs10231651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10234468	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10234685	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10245511	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10248070	1.00[JPT][hapmap]
rs10248443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10258269	1.00[JPT][hapmap]
rs10261308	1.00[JPT][hapmap]
rs10281362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11982615	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28464929	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28690889	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3852251	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs73683405	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777331	1.00[JPT][hapmap]
rs7798646	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9655161	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830917	chr7:18612436-18817712	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv531368	chr7:18677922-18836920	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv887814	chr7:18751998-18886177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2519739	HDAC9	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18790600-18835000	Weak transcription	Primary B cells from cord blood	blood
2	chr7:18808200-18823200	Weak transcription	Aorta	Aorta
3	chr7:18809600-18812600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:18810800-18821600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:18812000-18813000	Weak transcription	Osteobl	bone
6	chr7:18812000-18818000	Weak transcription	NHDF-Ad	bronchial
7	chr7:18812200-18817400	Weak transcription	HSMM	muscle
8	chr7:18812400-18817600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:18812400-18817800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:18812400-18826400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

Quick Search:

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

what's new

Quick links