Variant report

Variant	rs9563011
Chromosome Location	chr13:51473904-51473905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12583026	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12585449	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34164728	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34580649	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7993605	1.00[CEU][hapmap]
rs9563007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568490	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv900078	chr13:51454896-51478716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9563011	KPNA3	cis	parietal	SCAN
rs9563011	RNASEH2B	cis	Thyroid	GTEx
rs9563011	ITM2B	cis	parietal	SCAN
rs9563011	RNASEH2B	cis	brain	BrainEAC
rs9563011	RNASEH2B	cis	parietal	SCAN
rs9563011	FLJ11712	cis	multi-tissue	Pritchard
rs9563011	RNASEH2B	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51465600-51474600	Weak transcription	Aorta	Aorta
2	chr13:51469000-51483400	Weak transcription	Fetal Lung	lung
3	chr13:51471600-51474600	Weak transcription	Fetal Thymus	thymus
4	chr13:51471800-51474400	Enhancers	GM12878-XiMat	blood
5	chr13:51472000-51478200	Weak transcription	Thymus	Thymus
6	chr13:51472400-51474600	Weak transcription	Dnd41	blood
7	chr13:51472800-51474600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:51472800-51483400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:51473000-51474000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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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

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