Variant report

Variant	rs9824570
Chromosome Location	chr3:139733887-139733888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1025175	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13067861	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs13098635	0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes]
rs13315308	0.92[AMR][1000 genomes]
rs13322299	0.81[CEU][hapmap]
rs1365152	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398553	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398740	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2114167	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2162212	0.81[CEU][hapmap]
rs2350274	0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.92[AMR][1000 genomes]
rs6439892	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67276954	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71314533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356017	0.81[GIH][hapmap]
rs7433809	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7615793	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9289595	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813092	0.81[GIH][hapmap]
rs9813297	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9818578	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9824931	0.81[GIH][hapmap]
rs9827738	0.81[CEU][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9833263	0.81[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9835329	0.81[GIH][hapmap]
rs9845143	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9851415	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860322	0.81[GIH][hapmap]
rs9863333	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9870579	0.81[GIH][hapmap]
rs9878201	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9824570	SLC25A36	cis	cerebellum	SCAN
rs9824570	ESYT3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139714400-139741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139727600-139737200	Weak transcription	Ovary	ovary
3	chr3:139731800-139734200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:139732000-139739200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:139732400-139741200	Weak transcription	Fetal Brain Female	brain
6	chr3:139732400-139742600	Weak transcription	HSMMtube	muscle
7	chr3:139732800-139740200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:139733000-139739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:139733400-139734400	Enhancers	Brain Substantia Nigra	brain
10	chr3:139733800-139734200	Weak transcription	Fetal Brain Male	brain

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