Variant report

Variant	rs6889456
Chromosome Location	chr5:58360499-58360500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10066573	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10068543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514870	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12654485	0.87[CEU][hapmap]
rs13175380	0.87[EUR][1000 genomes]
rs13183985	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17720639	0.89[JPT][hapmap]
rs17776879	1.00[CHB][hapmap]
rs2021775	1.00[CEU][hapmap]
rs33927508	0.87[CEU][hapmap]
rs35859105	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450501	0.97[EUR][1000 genomes]
rs6450502	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6864156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71626132	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71626133	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707541	0.81[JPT][hapmap]
rs7737269	0.88[YRI][hapmap];1.00[AFR][1000 genomes]
rs950447	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs986067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58338800-58362000	Weak transcription	Gastric	stomach
3	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:58348200-58362000	Weak transcription	Psoas Muscle	Psoas
5	chr5:58349600-58360600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:58356400-58360800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58356600-58360800	Enhancers	HepG2	liver
8	chr5:58357400-58360600	Flanking Active TSS	A549	lung
9	chr5:58357600-58362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:58358000-58360600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:58358000-58361400	Weak transcription	NHEK	skin
12	chr5:58358200-58364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:58358200-58365000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58358400-58361400	Enhancers	NHDF-Ad	bronchial
15	chr5:58358400-58362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:58358600-58362600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:58358600-58362800	Enhancers	Osteobl	bone
18	chr5:58359400-58365200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:58359600-58364800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:58359800-58363200	Weak transcription	Fetal Lung	lung
21	chr5:58360000-58360600	Genic enhancers	Hela-S3	cervix
22	chr5:58360200-58360600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:58360200-58360600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr5:58360200-58360800	Enhancers	HMEC	breast
25	chr5:58360200-58361800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:58360200-58366000	Enhancers	HSMM	muscle
27	chr5:58360400-58365000	Weak transcription	Colon Smooth Muscle	Colon

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