Variant report

Variant	rs17005980
Chromosome Location	chr3:19494042-19494043
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10510495	0.83[ASN][1000 genomes]
rs10514672	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs10514673	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11543540	0.94[ASN][1000 genomes]
rs11561668	0.81[ASN][1000 genomes]
rs1348231	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372548	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1372551	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1442199	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17005936	1.00[CEU][hapmap]
rs17005937	1.00[CEU][hapmap]
rs17005949	1.00[CEU][hapmap]
rs17005954	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs17005967	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17005972	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17005976	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17005983	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs17005985	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs17005998	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006003	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17006048	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs17006054	0.84[ASN][1000 genomes]
rs17006062	0.84[ASN][1000 genomes]
rs4021207	1.00[CEU][hapmap]
rs57272811	0.81[ASN][1000 genomes]
rs57565118	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57684768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58915529	0.86[EUR][1000 genomes]
rs58996643	0.83[ASN][1000 genomes]
rs60546560	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60566663	0.84[ASN][1000 genomes]
rs60777133	0.87[ASN][1000 genomes]
rs60942804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61579329	0.82[ASN][1000 genomes]
rs6776448	1.00[CEU][hapmap]
rs6781615	0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs6796647	1.00[CEU][hapmap]
rs6800537	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6801951	1.00[CEU][hapmap]
rs7617994	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7626734	0.83[ASN][1000 genomes]
rs7626907	0.82[ASN][1000 genomes]
rs7649671	0.82[ASN][1000 genomes]
rs7653865	0.92[ASN][1000 genomes]
rs951678	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
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:8 , 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	chr3:19491200-19497000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:19491600-19494200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr3:19492000-19498200	Weak transcription	Primary B cells from cord blood	blood
7	chr3:19493800-19494200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr3:19493800-19496000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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