Variant report

Variant	rs17005983
Chromosome Location	chr3:19497353-19497354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10514672	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10514673	1.00[CEU][hapmap]
rs11543540	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1348231	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs1372548	1.00[CEU][hapmap]
rs1372551	1.00[CEU][hapmap];0.87[ASN][1000 genomes]
rs1442199	1.00[CEU][hapmap]
rs17005936	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17005937	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs17005949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs17005954	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs17005967	1.00[CEU][hapmap]
rs17005972	1.00[CEU][hapmap];0.84[CHD][hapmap]
rs17005976	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs17005980	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs17005985	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17005994	0.85[GIH][hapmap]
rs17005998	1.00[CEU][hapmap];0.87[CHD][hapmap]
rs17006003	1.00[CEU][hapmap]
rs17006010	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17006048	1.00[CEU][hapmap]
rs4021207	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[MEX][hapmap]
rs57575850	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58183288	0.90[EUR][1000 genomes]
rs6776448	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781577	0.85[GIH][hapmap]
rs6781615	0.88[CHB][hapmap];0.90[EUR][1000 genomes]
rs6796647	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800537	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6801951	1.00[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs7617994	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653865	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs951678	1.00[CEU][hapmap]
rs9841624	1.00[CEU][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	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv589855	chr3:19409153-19512074	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3386719	chr3:19454588-19895807	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19474400-19513200	Weak transcription	Brain Germinal Matrix	brain
2	chr3:19480400-19514400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:19480600-19498400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:19492000-19498200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:19494200-19498000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:19494200-19498200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:19496000-19499400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:19497000-19497400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:19497000-19498200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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