Variant report

Variant	rs62399939
Chromosome Location	chr6:53614849-53614850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11759427	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11759473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662433	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4478409	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712042	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4715421	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57853292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458956	0.99[ASN][1000 genomes]
rs7759593	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9463970	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9463971	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463975	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463976	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474643	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474647	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474650	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474651	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
3	chr6:53612200-53616200	Weak transcription	HMEC	breast
4	chr6:53612200-53616600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:53612200-53616800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:53612200-53617400	Weak transcription	Placenta	Placenta
7	chr6:53614000-53617000	Enhancers	Brain Germinal Matrix	brain
8	chr6:53614000-53618200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:53614400-53615800	Enhancers	Fetal Brain Male	brain
10	chr6:53614600-53615800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:53614800-53615000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:53614800-53615400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:53614800-53615600	Enhancers	NHEK	skin
14	chr6:53614800-53615800	Enhancers	Hela-S3	cervix
15	chr6:53614800-53618800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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