Variant report

Variant	rs1973921
Chromosome Location	chr20:24985657-24985658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24985071..24988869-chr20:24990703..24995644,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3928737	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6037006	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6050244	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6083718	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6114995	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6114996	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][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	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24974000-24985800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr20:24974000-24985800	Weak transcription	Thymus	Thymus
3	chr20:24974000-24986400	Weak transcription	Aorta	Aorta
4	chr20:24974200-24985800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr20:24974200-24988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:24974400-24992000	Weak transcription	GM12878-XiMat	blood
7	chr20:24974800-24985800	Weak transcription	Spleen	Spleen
8	chr20:24975800-24986400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr20:24976000-24985800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr20:24976000-24985800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr20:24976000-24986000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr20:24976000-24986000	Weak transcription	Colonic Mucosa	Colon
13	chr20:24976000-24986400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr20:24976000-24986400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:24976000-24987600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr20:24976000-24988000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr20:24976200-24985800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr20:24976200-24985800	Weak transcription	Adipose Nuclei	Adipose
20	chr20:24976200-24985800	Weak transcription	Lung	lung
21	chr20:24976200-24986200	Weak transcription	Dnd41	blood
22	chr20:24976800-24986000	Weak transcription	Brain Germinal Matrix	brain
23	chr20:24977000-24986600	Weak transcription	Fetal Thymus	thymus
24	chr20:24979000-24987400	Weak transcription	Small Intestine	intestine
25	chr20:24979400-24986000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr20:24980000-24985800	Weak transcription	Gastric	stomach
27	chr20:24980600-24986200	Weak transcription	Right Atrium	heart
28	chr20:24981200-24985800	Weak transcription	Brain Substantia Nigra	brain
29	chr20:24981200-24986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr20:24981200-24986600	Weak transcription	Esophagus	oesophagus
31	chr20:24981400-24985800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr20:24981400-24986200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:24981400-24986600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr20:24981600-24986000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr20:24981600-24986000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr20:24981600-24986200	Weak transcription	Brain Anterior Caudate	brain
37	chr20:24981600-24986400	Weak transcription	Brain Hippocampus Middle	brain
38	chr20:24981600-24986400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr20:24981600-24987400	Weak transcription	Stomach Mucosa	stomach
40	chr20:24981600-24989600	Weak transcription	Brain Angular Gyrus	brain
41	chr20:24981600-25003600	Weak transcription	Fetal Heart	heart
42	chr20:24981800-24985800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr20:24981800-24986000	Weak transcription	Pancreas	Pancrea
44	chr20:24981800-24986200	Weak transcription	Right Ventricle	heart
45	chr20:24981800-24986600	Weak transcription	Ovary	ovary
46	chr20:24981800-24987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:24981800-24987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:24981800-24988200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:24981800-24989800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr20:24981800-24992600	Weak transcription	Psoas Muscle	Psoas

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