Variant report

Variant	rs3846052
Chromosome Location	chr3:134138009-134138010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134137781..134139924-chr3:134140721..134142548,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10935116	1.00[CHB][hapmap]
rs11707704	1.00[ASN][1000 genomes]
rs11917363	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11919447	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11923513	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11928672	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11928742	1.00[CHB][hapmap]
rs11928907	1.00[ASN][1000 genomes]
rs12487438	1.00[CHB][hapmap]
rs13069766	1.00[ASN][1000 genomes]
rs13071132	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13079012	1.00[CHD][hapmap]
rs13084853	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13090504	1.00[ASN][1000 genomes]
rs1498730	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17312996	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17313003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34006849	1.00[ASN][1000 genomes]
rs34524468	1.00[ASN][1000 genomes]
rs34549392	1.00[ASN][1000 genomes]
rs35098409	1.00[ASN][1000 genomes]
rs35471660	1.00[ASN][1000 genomes]
rs35527623	1.00[ASN][1000 genomes]
rs35558600	1.00[ASN][1000 genomes]
rs35878592	1.00[ASN][1000 genomes]
rs3913262	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339087	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5002434	1.00[ASN][1000 genomes]
rs5002435	1.00[ASN][1000 genomes]
rs5002436	1.00[ASN][1000 genomes]
rs5002437	1.00[ASN][1000 genomes]
rs55682444	1.00[ASN][1000 genomes]
rs56019901	1.00[ASN][1000 genomes]
rs59458665	1.00[ASN][1000 genomes]
rs61145443	1.00[ASN][1000 genomes]
rs62271221	1.00[ASN][1000 genomes]
rs6439474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6439476	1.00[ASN][1000 genomes]
rs6768709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6772791	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6776727	1.00[ASN][1000 genomes]
rs6804439	1.00[ASN][1000 genomes]
rs6809909	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71331755	1.00[ASN][1000 genomes]
rs72986454	1.00[ASN][1000 genomes]
rs73215399	1.00[ASN][1000 genomes]
rs7609766	1.00[ASN][1000 genomes]
rs7613323	1.00[ASN][1000 genomes]
rs7613440	1.00[ASN][1000 genomes]
rs7613450	1.00[ASN][1000 genomes]
rs7614069	1.00[ASN][1000 genomes]
rs7636249	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7637889	1.00[CHB][hapmap]
rs7638751	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7642519	1.00[ASN][1000 genomes]
rs7647682	1.00[CHB][hapmap]
rs7647778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7651578	1.00[ASN][1000 genomes]
rs9826364	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1007607	chr3:134131521-134156814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3846052	BPESC1	cis	parietal	SCAN
rs3846052	CCRL1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134126400-134141800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:134126400-134146000	Weak transcription	Pancreas	Pancrea
3	chr3:134129600-134138200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:134137600-134138200	Enhancers	HepG2	liver
5	chr3:134137800-134139400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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