Variant report

Variant	rs17005985
Chromosome Location	chr3:19498482-19498483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514672	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs10514673	1.00[CEU][hapmap]
rs11543540	0.90[EUR][1000 genomes]
rs1348231	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1372548	1.00[CEU][hapmap]
rs1372551	1.00[CEU][hapmap];0.91[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];0.90[EUR][1000 genomes]
rs17005949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs17005954	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs17005967	1.00[CEU][hapmap]
rs17005972	1.00[CEU][hapmap]
rs17005976	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17005980	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs17005983	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]
rs17005998	1.00[CEU][hapmap]
rs17006003	1.00[CEU][hapmap]
rs17006010	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs17006048	1.00[CEU][hapmap]
rs4021207	1.00[CEU][hapmap]
rs57575850	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58183288	0.90[EUR][1000 genomes]
rs6776448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781615	0.90[EUR][1000 genomes]
rs6796647	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800537	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6801951	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs7617994	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653865	0.82[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:20 , 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	chr3:19496000-19499400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:19498000-19498600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:19498000-19499200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:19498000-19499400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:19498000-19499400	Enhancers	Brain Substantia Nigra	brain
8	chr3:19498000-19499600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:19498200-19498600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:19498200-19498600	Enhancers	Adipose Nuclei	Adipose
11	chr3:19498200-19499200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:19498200-19499200	Strong transcription	Primary B cells from cord blood	blood
13	chr3:19498200-19499600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:19498200-19499600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:19498200-19499600	Enhancers	HMEC	breast
16	chr3:19498200-19500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:19498200-19500400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:19498200-19501200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:19498400-19499400	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:19498400-19499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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