Variant report

Variant	rs66940098
Chromosome Location	chr9:8662484-8662485
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1025548	0.87[AFR][1000 genomes]
rs17652834	0.91[EUR][1000 genomes]
rs2137346	0.81[EUR][1000 genomes]
rs2137347	0.81[EUR][1000 genomes]
rs55855913	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56003760	0.82[EUR][1000 genomes]
rs56158447	0.81[EUR][1000 genomes]
rs72698237	0.81[EUR][1000 genomes]
rs72698247	0.83[EUR][1000 genomes]
rs72698258	0.84[EUR][1000 genomes]
rs72700314	0.82[EUR][1000 genomes]
rs72700318	0.86[EUR][1000 genomes]
rs72700328	0.86[EUR][1000 genomes]
rs72700332	0.88[EUR][1000 genomes]
rs7868744	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv892232	chr9:8645448-8698875	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892233	chr9:8645448-8702964	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv892234	chr9:8645448-8703733	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3350587	chr9:8660042-8663346	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	esv3481888	chr9:8660111-8663285	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
10	esv3481889	chr9:8660111-8663285	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8652800-8664400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:8652800-8669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:8653800-8664800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:8659800-8662600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:8660600-8668000	Weak transcription	Fetal Brain Female	brain
6	chr9:8660800-8663600	Weak transcription	Ovary	ovary
7	chr9:8660800-8672400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:8661000-8664400	Weak transcription	Brain Substantia Nigra	brain
9	chr9:8661000-8666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:8661200-8664400	Weak transcription	Brain Anterior Caudate	brain
11	chr9:8661200-8664600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:8661400-8664000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:8661400-8664400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:8661400-8666200	Weak transcription	Liver	Liver
15	chr9:8661400-8668800	Weak transcription	Fetal Brain Male	brain
16	chr9:8661400-8677400	Weak transcription	Brain Angular Gyrus	brain
17	chr9:8661600-8664200	Weak transcription	Fetal Heart	heart
18	chr9:8662000-8662800	Enhancers	Brain Hippocampus Middle	brain
19	chr9:8662400-8662600	Enhancers	Adipose Nuclei	Adipose

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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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