Variant report

Variant	rs28698664
Chromosome Location	chr3:139673131-139673132
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11927306	0.81[AMR][1000 genomes]
rs35018094	0.83[EUR][1000 genomes]
rs7356017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7433927	0.81[AMR][1000 genomes]
rs9810814	0.81[AMR][1000 genomes]
rs9813092	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821561	0.81[AMR][1000 genomes]
rs9821898	0.83[EUR][1000 genomes]
rs9824300	0.83[EUR][1000 genomes]
rs9835329	0.82[EUR][1000 genomes]
rs9852679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9860322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870392	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv877544	chr3:139642572-139688415	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv460866	chr3:139661938-139704174	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv591859	chr3:139661938-139704174	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139668200-139698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139669200-139682200	Weak transcription	HSMMtube	muscle
3	chr3:139671200-139673800	Enhancers	HMEC	breast
4	chr3:139671600-139673400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:139671600-139673600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:139671800-139673400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:139671800-139673600	Enhancers	NHEK	skin
8	chr3:139672200-139673600	Enhancers	Ovary	ovary
9	chr3:139672800-139673200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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