Variant report

Variant	rs17720871
Chromosome Location	chr5:58363900-58363901
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58363195..58365401-chr5:58365586..58367971,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10065303	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10452450	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10514871	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1115728	1.00[JPT][hapmap]
rs12109774	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs16889167	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs17720311	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17720639	0.82[EUR][1000 genomes]
rs17721133	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721311	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721564	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17721878	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17776825	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17777280	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]
rs17777617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244458	0.83[EUR][1000 genomes]
rs55801062	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56057207	0.91[AFR][1000 genomes]
rs56407743	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356683	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356684	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356686	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62356687	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62356690	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62356691	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62356692	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898082	1.00[JPT][hapmap]
rs7707541	0.83[EUR][1000 genomes]
rs950446	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.99[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:26 , 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	chr5:58359400-58365200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58359600-58364800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:58360200-58366000	Enhancers	HSMM	muscle
8	chr5:58360400-58365000	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:58360600-58373800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:58360800-58367200	Weak transcription	HepG2	liver
11	chr5:58361000-58365800	Enhancers	HSMMtube	muscle
12	chr5:58362200-58366000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:58362400-58364200	Weak transcription	NHDF-Ad	bronchial
14	chr5:58362400-58364200	Weak transcription	NHLF	lung
15	chr5:58362400-58368200	Weak transcription	Psoas Muscle	Psoas
16	chr5:58362600-58364400	Weak transcription	HMEC	breast
17	chr5:58362600-58365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:58362800-58364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:58362800-58365000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:58362800-58365000	Weak transcription	NH-A	brain
21	chr5:58363000-58364200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:58363200-58364000	Genic enhancers	Hela-S3	cervix
23	chr5:58363200-58364200	Enhancers	Fetal Lung	lung
24	chr5:58363400-58364400	Transcr. at gene 5' and 3'	A549	lung
25	chr5:58363800-58364000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:58363800-58364000	Enhancers	Right Ventricle	heart

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