Variant report

Variant	rs56020939
Chromosome Location	chr5:54041375-54041376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53812268..53814960-chr5:54041334..54044388,3	MCF-7	breast:
2	chr5:54037843..54041857-chr5:54043536..54048349,6	K562	blood:
3	chr5:54040322..54042008-chr5:54061113..54064039,2	K562	blood:
4	chr5:54039960..54041992-chr5:54042143..54044677,2	K562	blood:

Variant related genes	Relation type
ENSG00000178996	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1867688	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56146444	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58082608	0.81[EUR][1000 genomes]
rs6450241	0.80[EUR][1000 genomes]
rs6869164	0.83[EUR][1000 genomes]
rs72757405	0.80[EUR][1000 genomes]
rs72757411	0.80[EUR][1000 genomes]
rs72757433	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757436	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757442	1.00[ASN][1000 genomes]
rs72762223	1.00[ASN][1000 genomes]
rs72762225	1.00[ASN][1000 genomes]
rs72762245	1.00[ASN][1000 genomes]
rs7714829	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880717	chr5:54025701-54106378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3378305	chr5:54040695-54045193	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54034600-54041400	Weak transcription	Lung	lung
2	chr5:54036400-54041600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:54036400-54042000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:54036800-54041800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:54036800-54044800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:54037200-54042800	Weak transcription	Gastric	stomach
7	chr5:54037600-54041400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:54037600-54042000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:54037800-54041600	Enhancers	NHLF	lung
10	chr5:54038200-54041400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr5:54038200-54041600	Enhancers	HSMM	muscle
12	chr5:54038200-54041800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:54038200-54041800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:54038200-54041800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:54038200-54041800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr5:54038200-54041800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:54038200-54041800	Enhancers	Fetal Heart	heart
18	chr5:54038200-54042000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr5:54038200-54042600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:54038400-54041600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:54038400-54041800	Enhancers	Fetal Lung	lung
22	chr5:54038400-54042800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr5:54038600-54041600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr5:54038600-54041600	Weak transcription	Left Ventricle	heart
25	chr5:54038600-54041800	Enhancers	Duodenum Mucosa	Duodenum
26	chr5:54038800-54041400	Weak transcription	Pancreas	Pancrea
27	chr5:54039000-54041600	Enhancers	Primary hematopoietic stem cells	blood
28	chr5:54039000-54042000	Enhancers	Dnd41	blood
29	chr5:54039400-54041800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:54039600-54041400	Enhancers	Primary B cells from cord blood	blood
31	chr5:54039600-54041600	Enhancers	Primary B cells from peripheral blood	blood
32	chr5:54039600-54041800	Enhancers	Fetal Thymus	thymus
33	chr5:54039600-54042000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:54039600-54042600	Enhancers	Spleen	Spleen
35	chr5:54039800-54041400	Enhancers	Fetal Intestine Small	intestine
36	chr5:54039800-54041400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr5:54039800-54041600	Enhancers	Fetal Intestine Large	intestine
38	chr5:54039800-54041800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:54040000-54041600	Weak transcription	Small Intestine	intestine
40	chr5:54040000-54042000	Enhancers	NHDF-Ad	bronchial
41	chr5:54040000-54043000	Weak transcription	Right Ventricle	heart
42	chr5:54040200-54044600	Weak transcription	Esophagus	oesophagus
43	chr5:54040600-54041400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:54040600-54041400	Enhancers	HSMMtube	muscle
45	chr5:54040600-54041600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:54040600-54041600	Weak transcription	Placenta	Placenta
47	chr5:54040600-54041600	Enhancers	GM12878-XiMat	blood
48	chr5:54040600-54041800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:54040600-54041800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:54040600-54042000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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