Variant report

Variant	rs17777280
Chromosome Location	chr5:58362303-58362304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10065303	0.88[CEU][hapmap]
rs10452450	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs10514871	1.00[YRI][hapmap]
rs1115728	1.00[JPT][hapmap]
rs12109774	0.96[CEU][hapmap]
rs16889167	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17720311	1.00[YRI][hapmap]
rs17720639	0.81[EUR][1000 genomes]
rs17720871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721564	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs17721878	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17776825	1.00[YRI][hapmap]
rs17777617	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244458	0.81[EUR][1000 genomes]
rs55801062	0.85[ASN][1000 genomes]
rs56407743	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356680	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356683	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356684	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356686	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62356687	0.82[AMR][1000 genomes]
rs62356690	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62356691	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62356692	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6898082	1.00[JPT][hapmap]
rs7707541	0.82[EUR][1000 genomes]
rs950446	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58358200-58364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:58358200-58365000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:58358400-58362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:58358600-58362600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:58358600-58362800	Enhancers	Osteobl	bone
8	chr5:58359400-58365200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:58359600-58364800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:58359800-58363200	Weak transcription	Fetal Lung	lung
11	chr5:58360200-58366000	Enhancers	HSMM	muscle
12	chr5:58360400-58365000	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:58360600-58362800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:58360600-58363200	Enhancers	Hela-S3	cervix
15	chr5:58360600-58373800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:58360800-58362800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:58360800-58367200	Weak transcription	HepG2	liver
18	chr5:58361000-58365800	Enhancers	HSMMtube	muscle
19	chr5:58361400-58362400	Enhancers	NHEK	skin
20	chr5:58361800-58362400	Enhancers	NHDF-Ad	bronchial
21	chr5:58361800-58362400	Enhancers	NHLF	lung
22	chr5:58361800-58362600	Enhancers	HMEC	breast
23	chr5:58362000-58362400	Enhancers	Gastric	stomach
24	chr5:58362000-58362400	Enhancers	Right Ventricle	heart
25	chr5:58362000-58362400	Transcr. at gene 5' and 3'	A549	lung
26	chr5:58362000-58362800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:58362000-58362800	Enhancers	NH-A	brain
28	chr5:58362000-58363000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:58362200-58362400	Enhancers	Psoas Muscle	Psoas
30	chr5:58362200-58362600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:58362200-58366000	Enhancers	Muscle Satellite Cultured Cells	--

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