Variant report

Variant	rs1025547
Chromosome Location	chr9:8664838-8664839
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1025548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337808	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7851001	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs907625	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1025547	RLN1	cis	parietal	SCAN
rs1025547	PDCD1LG2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8652800-8669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:8660600-8668000	Weak transcription	Fetal Brain Female	brain
3	chr9:8660800-8672400	Weak transcription	Brain Germinal Matrix	brain
4	chr9:8661000-8666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:8661400-8666200	Weak transcription	Liver	Liver
6	chr9:8661400-8668800	Weak transcription	Fetal Brain Male	brain
7	chr9:8661400-8677400	Weak transcription	Brain Angular Gyrus	brain
8	chr9:8664200-8665400	Enhancers	Fetal Heart	heart
9	chr9:8664400-8665000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr9:8664400-8665200	Enhancers	Brain Hippocampus Middle	brain
11	chr9:8664400-8665600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:8664400-8666000	Enhancers	Brain Substantia Nigra	brain
13	chr9:8664600-8665000	Weak transcription	Brain Anterior Caudate	brain
14	chr9:8664600-8665600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:8664600-8668800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:8664800-8666200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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