Variant report

Variant	rs17516489
Chromosome Location	chr2:62775464-62775465
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10496098	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11900958	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1527962	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17516315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17516336	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17575420	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17575679	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2901483	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56185926	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56390862	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62178040	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62178041	0.81[EUR][1000 genomes]
rs62178044	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62178045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62178046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62178047	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3336776	chr2:62747914-62813461	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17516489	TMEM17	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62772800-62783200	Weak transcription	Pancreas	Pancrea
2	chr2:62773000-62781600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:62773400-62777200	Weak transcription	NHDF-Ad	bronchial
4	chr2:62774600-62775600	Enhancers	Fetal Intestine Small	intestine
5	chr2:62775200-62775600	Enhancers	HepG2	liver
6	chr2:62775400-62777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte 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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