Variant report

Variant	rs58083478
Chromosome Location	chr20:25040424-25040425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25032527..25035027-chr20:25040068..25042955,2	K562	blood:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:25030752..25032686-chr20:25040138..25042817,2	MCF-7	breast:
4	chr20:25039944..25042062-chr20:25044050..25046004,2	K562	blood:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11904887	0.86[AFR][1000 genomes]
rs11908084	0.84[AFR][1000 genomes]
rs59731128	1.00[AFR][1000 genomes]
rs60687375	0.94[AFR][1000 genomes]
rs7273872	1.00[AFR][1000 genomes]
rs73331209	0.96[AFR][1000 genomes]
rs73331224	0.90[AFR][1000 genomes]
rs73348752	0.96[AFR][1000 genomes]
rs73348757	1.00[AFR][1000 genomes]
rs73348773	0.96[AFR][1000 genomes]
rs8118553	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25039400-25041000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:25039600-25040600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr20:25039600-25040800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:25039600-25041000	Enhancers	Fetal Muscle Trunk	muscle
5	chr20:25039600-25041000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr20:25039600-25041800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:25039600-25042800	Enhancers	Gastric	stomach
8	chr20:25039600-25044600	Enhancers	Pancreas	Pancrea
9	chr20:25039600-25044800	Weak transcription	Brain Anterior Caudate	brain
10	chr20:25039600-25044800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr20:25039800-25040600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:25039800-25040600	Enhancers	Colon Smooth Muscle	Colon
13	chr20:25039800-25040600	Enhancers	Fetal Thymus	thymus
14	chr20:25039800-25040800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr20:25039800-25040800	Enhancers	Fetal Muscle Leg	muscle
16	chr20:25039800-25041400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:25039800-25041400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:25039800-25042200	Bivalent Enhancer	HepG2	liver
19	chr20:25039800-25043200	Enhancers	Fetal Intestine Small	intestine
20	chr20:25039800-25044800	Weak transcription	Right Ventricle	heart
21	chr20:25039800-25045400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr20:25040000-25040600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr20:25040000-25040600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr20:25040000-25040800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr20:25040000-25040800	Enhancers	Primary hematopoietic stem cells	blood
26	chr20:25040000-25040800	Enhancers	Thymus	Thymus
27	chr20:25040000-25041000	Enhancers	GM12878-XiMat	blood
28	chr20:25040000-25042800	Enhancers	Stomach Mucosa	stomach
29	chr20:25040200-25040600	Enhancers	Stomach Smooth Muscle	stomach
30	chr20:25040200-25040800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:25040200-25040800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr20:25040200-25040800	Enhancers	Dnd41	blood
33	chr20:25040200-25041600	Weak transcription	Liver	Liver
34	chr20:25040200-25045200	Weak transcription	Brain Hippocampus Middle	brain
35	chr20:25040200-25045200	Weak transcription	Left Ventricle	heart
36	chr20:25040200-25046000	Weak transcription	Spleen	Spleen
37	chr20:25040400-25041400	Weak transcription	Fetal Intestine Large	intestine
38	chr20:25040400-25041600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr20:25040400-25042400	Weak transcription	Primary B cells from cord blood	blood
40	chr20:25040400-25042400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr20:25040400-25042600	Weak transcription	Placenta	Placenta
42	chr20:25040400-25045200	Weak transcription	Brain Cingulate Gyrus	brain

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