Variant report

Variant	rs9638636
Chromosome Location	chr7:71299787-71299788
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10226380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950280	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12673420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56854782	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7777622	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7804470	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9638635	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1027496	chr7:71162362-71575116	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9638636	CLDN3	cis	cerebellum	SCAN
rs9638636	CLDN4	cis	cerebellum	SCAN
rs9638636	CLIP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71275800-71300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:71292200-71307000	Weak transcription	Fetal Thymus	thymus
3	chr7:71292400-71308200	Weak transcription	Thymus	Thymus
4	chr7:71292400-71308800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:71294800-71301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:71298200-71302000	Weak transcription	Right Atrium	heart
7	chr7:71299600-71300200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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