Variant report

Variant	rs12516817
Chromosome Location	chr5:119629679-119629680
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11241541	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11241544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953656	0.86[AMR][1000 genomes]
rs12514405	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521979	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655926	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12655927	0.86[AMR][1000 genomes]
rs12655944	0.86[AMR][1000 genomes]
rs13171088	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13188486	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422391	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2405803	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35139304	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36047600	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36064957	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36079833	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66864061	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6886288	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71586476	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv432803	chr5:119419101-119659101	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv882786	chr5:119615110-119714817	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv965575	chr5:119621540-119650309	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119628000-119630600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:119628200-119632000	Enhancers	NHDF-Ad	bronchial
3	chr5:119629000-119629800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:119629000-119630200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:119629000-119630400	Enhancers	HMEC	breast
6	chr5:119629200-119629800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:119629200-119629800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:119629200-119630200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:119629200-119630200	Enhancers	NHEK	skin
10	chr5:119629200-119630200	Enhancers	NHLF	lung
11	chr5:119629200-119630400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:119629200-119630400	Enhancers	HSMM	muscle
13	chr5:119629200-119630400	Enhancers	NH-A	brain
14	chr5:119629200-119630400	Enhancers	Osteobl	bone
15	chr5:119629600-119630400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:119629600-119632400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:119629600-119632600	Weak transcription	HSMMtube	muscle
18	chr5:119629600-119632800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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Input of quick search could be:

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

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