Variant report

Variant	rs62257339
Chromosome Location	chr3:86983897-86983898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17023658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232714	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62257279	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62257280	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62257281	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62257283	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62257314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257346	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62259360	0.82[AMR][1000 genomes]
rs62259363	0.82[AMR][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	nsv519148	chr3:86831077-86995124	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 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	chr3:86972600-86986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:86973400-86986200	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:86973600-86986000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:86979000-86986200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:86980200-86985800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:86980400-86984800	Weak transcription	Osteobl	bone
7	chr3:86980400-86985800	Weak transcription	HSMM	muscle
8	chr3:86980600-86986400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:86980600-86995600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:86981000-86985800	Weak transcription	NHDF-Ad	bronchial
11	chr3:86981600-86985200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:86981800-86987000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:86982000-86986000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:86982800-86984600	Enhancers	HSMMtube	muscle
15	chr3:86983000-86985200	Weak transcription	NHLF	lung
16	chr3:86983600-86985800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:86983800-86986200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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