Variant report

Variant	rs7643842
Chromosome Location	chr3:21488446-21488447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12638887	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13061028	0.87[JPT][hapmap]
rs13095088	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs341850	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs341852	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs341853	0.81[ASN][1000 genomes]
rs341854	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs368255	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs3732905	0.82[CHB][hapmap]
rs3821733	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3849537	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3849539	0.81[CHB][hapmap]
rs3860572	0.81[CHB][hapmap]
rs4085212	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs453364	0.89[ASN][1000 genomes]
rs4857999	0.87[CHB][hapmap]
rs4858000	0.87[CHB][hapmap]
rs4858002	0.86[CHB][hapmap]
rs6550607	0.86[CHB][hapmap]
rs6774929	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6787052	0.85[EUR][1000 genomes]
rs6787456	0.87[CHB][hapmap]
rs6787955	0.86[ASN][1000 genomes]
rs6797692	0.86[CHB][hapmap]
rs6806788	0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7611710	0.82[CHB][hapmap]
rs7614523	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625365	0.82[CHB][hapmap]
rs9809197	0.81[CHB][hapmap]
rs9819691	0.82[AFR][1000 genomes]
rs9838377	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9874351	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9879872	0.85[CHB][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9883841	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834630	chr3:21311619-21491327	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1006471	chr3:21385627-21596955	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1000828	chr3:21399870-21565580	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536515	chr3:21399870-21565580	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21463000-21491400	Weak transcription	Aorta	Aorta
2	chr3:21477000-21491200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:21477000-21507200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:21477400-21488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:21478800-21488600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:21480000-21489000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:21483600-21491200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:21487600-21489200	Enhancers	Fetal Stomach	stomach
9	chr3:21487800-21488800	Weak transcription	Fetal Brain Female	brain
10	chr3:21488000-21488600	Enhancers	Ovary	ovary
11	chr3:21488000-21488800	Weak transcription	Fetal Lung	lung
12	chr3:21488400-21488800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:21488400-21489400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:21488400-21489400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:21488400-21489400	Flanking Active TSS	NHDF-Ad	bronchial
16	chr3:21488400-21490200	Enhancers	HSMM	muscle
17	chr3:21488400-21491200	Weak transcription	Left Ventricle	heart

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