Variant report

Variant	rs9568490
Chromosome Location	chr13:51469798-51469799
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12583026	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12585449	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34164728	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34580649	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41292768	0.84[AFR][1000 genomes]
rs57199709	0.84[AFR][1000 genomes]
rs61333791	0.81[AFR][1000 genomes]
rs61962174	0.84[AFR][1000 genomes]
rs61962189	0.84[AFR][1000 genomes]
rs61962202	0.84[AFR][1000 genomes]
rs7330305	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7993605	1.00[CEU][hapmap]
rs9563007	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9563008	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9563010	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9563011	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9568490	KPNA3	cis	parietal	SCAN
rs9568490	ITM2B	cis	parietal	SCAN
rs9568490	FLJ11712	cis	multi-tissue	Pritchard
rs9568490	RNASEH2B	cis	parietal	SCAN
rs9568490	RNASEH2B	cis	cerebellum	SCAN
rs9568490	RNASEH2B	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51465600-51474600	Weak transcription	Aorta	Aorta
2	chr13:51466600-51471000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr13:51467200-51470200	Flanking Active TSS	Dnd41	blood
4	chr13:51467800-51470800	Enhancers	Primary hematopoietic stem cells	blood
5	chr13:51468400-51471400	Enhancers	Thymus	Thymus
6	chr13:51468800-51472000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:51468800-51472200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr13:51468800-51472200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr13:51468800-51472200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr13:51469000-51471000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:51469000-51483400	Weak transcription	Fetal Lung	lung
12	chr13:51469200-51471800	Weak transcription	GM12878-XiMat	blood
13	chr13:51469200-51472000	Weak transcription	Fetal Heart	heart
14	chr13:51469400-51470200	Genic enhancers	Fetal Thymus	thymus
15	chr13:51469600-51470800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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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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