Variant report

Variant	rs9390434
Chromosome Location	chr6:147189967-147189968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1022877	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs1122570	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1324684	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1467623	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1966195	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1998641	0.83[JPT][hapmap]
rs4605907	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4895704	0.88[JPT][hapmap]
rs4896895	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724774	0.83[JPT][hapmap]
rs7752595	0.82[YRI][hapmap]
rs877660	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs912577	0.88[JPT][hapmap]
rs912580	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9373515	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390436	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9390434	KATNA1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147179600-147192200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:147182200-147197600	Weak transcription	Pancreas	Pancrea
3	chr6:147182800-147193000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:147185400-147192000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:147185800-147191200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:147186000-147191400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:147186200-147191600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:147186400-147192800	Weak transcription	Esophagus	oesophagus
9	chr6:147189200-147190400	Enhancers	Liver	Liver
10	chr6:147189800-147196400	Enhancers	K562	blood

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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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