Variant report

Variant	rs9808243
Chromosome Location	chr2:86875548-86875549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86864508..86866719-chr2:86874258..86877076,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10165914	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176028	0.85[EUR][1000 genomes]
rs10178968	0.88[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184617	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10197478	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206802	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051386	0.80[CEU][hapmap]
rs11127049	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895434	0.86[EUR][1000 genomes]
rs12477737	0.86[ASN][1000 genomes]
rs12613610	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[ASN][1000 genomes]
rs13407663	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370452	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437615	0.86[EUR][1000 genomes]
rs2138397	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs3020729	0.80[CEU][hapmap]
rs308920	0.88[ASN][1000 genomes]
rs308921	0.91[ASN][1000 genomes]
rs36100635	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs4423596	0.85[EUR][1000 genomes]
rs4832047	0.91[ASN][1000 genomes]
rs4832048	0.83[ASN][1000 genomes]
rs4832306	0.91[ASN][1000 genomes]
rs58333815	0.81[EUR][1000 genomes]
rs59818518	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6547701	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709371	0.84[EUR][1000 genomes]
rs6758373	0.86[EUR][1000 genomes]
rs72934456	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934463	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72934466	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7425154	0.88[CEU][hapmap]
rs7558827	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7564251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9808243	POLR1A	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86873800-86875800	Weak transcription	Stomach Mucosa	stomach
2	chr2:86875000-86876800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
3	chr2:86875000-86877000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:86875200-86876000	Enhancers	Liver	Liver
5	chr2:86875200-86876000	Weak transcription	Pancreas	Pancrea
6	chr2:86875200-86876000	Enhancers	HepG2	liver

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