Variant report

Variant	rs10961996
Chromosome Location	chr9:15370832-15370833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10810385	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10961984	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10961998	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12554140	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62572991	0.83[EUR][1000 genomes]
rs7045886	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10961996	SNAPC3	cis	cerebellum	SCAN
rs10961996	NFIB	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15369000-15374800	Enhancers	Fetal Lung	lung
2	chr9:15370400-15371200	Enhancers	Fetal Brain Male	brain
3	chr9:15370400-15371200	Enhancers	Fetal Brain Female	brain
4	chr9:15370400-15371800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr9:15370600-15371200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:15370600-15371200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:15370600-15371600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:15370600-15373000	Enhancers	Ovary	ovary
9	chr9:15370800-15371000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:15370800-15371000	Enhancers	HepG2	liver
11	chr9:15370800-15371200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr9:15370800-15371400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:15370800-15374600	Enhancers	Fetal Intestine Large	intestine

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

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