Variant report

Variant	rs58979406
Chromosome Location	chr20:52487014-52487015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52193542..52196598-chr20:52485372..52487556,88	MCF-7	breast:
2	chr20:52401639..52403990-chr20:52486019..52487230,15	MCF-7	breast:
3	chr20:52407146..52408072-chr20:52486248..52487589,4	MCF-7	breast:
4	chr20:52405785..52406558-chr20:52486542..52487158,2	MCF-7	breast:
5	chr17:57161263..57162769-chr20:52485714..52488362,2	MCF-7	breast:
6	chr12:66506885..66508576-chr20:52484476..52487409,2	MCF-7	breast:
7	chr17:57919387..57922338-chr20:52486678..52488392,3	MCF-7	breast:
8	chr20:52404006..52404610-chr20:52486214..52487190,2	MCF-7	breast:
9	chr17:59491669..59494227-chr20:52486642..52489549,2	MCF-7	breast:
10	chr20:52194976..52196071-chr20:52485853..52487276,31	MCF-7	breast:
11	chr20:52373423..52374345-chr20:52486500..52487026,2	MCF-7	breast:
12	chr20:52486059..52487240-chr20:55798532..55799173,4	MCF-7	breast:
13	chr14:71787305..71788925-chr20:52486960..52489477,2	MCF-7	breast:
14	chr20:52479383..52482682-chr20:52485789..52487570,3	K562	blood:
15	chr20:52478179..52488683-chr20:55835744..55846940,26	MCF-7	breast:
16	chr20:52485674..52487205-chr20:52555803..52557075,17	MCF-7	breast:
17	chr17:59494815..59495425-chr20:52486734..52487494,2	MCF-7	breast:
18	chr20:52481182..52483675-chr20:52485548..52487289,2	K562	blood:
19	chr20:52485183..52487690-chrX:47516398..47518387,2	MCF-7	breast:
20	chr20:52486203..52487509-chr20:52555822..52557169,7	MCF-7	breast:
21	chr20:52471901..52491673-chr20:55835708..55845674,34	MCF-7	breast:
22	chr20:52486123..52487483-chr20:52531651..52533119,11	MCF-7	breast:
23	chr20:52229027..52230007-chr20:52485802..52487058,7	MCF-7	breast:
24	chr17:57914372..57916442-chr20:52486421..52488125,2	MCF-7	breast:
25	chr20:52417799..52418600-chr20:52486609..52487141,2	MCF-7	breast:
26	chr20:52485654..52487265-chr20:52530091..52533503,52	MCF-7	breast:
27	chr17:56707630..56709159-chr20:52486995..52489742,2	MCF-7	breast:
28	chr17:57923074..57925214-chr20:52484890..52487156,2	MCF-7	breast:
29	chr20:52390064..52391133-chr20:52486352..52487037,3	MCF-7	breast:
30	chr20:52224263..52224919-chr20:52486339..52487302,2	MCF-7	breast:
31	chr20:52486423..52487978-chr20:52491566..52493506,2	K562	blood:
32	chr20:52229047..52230576-chr20:52485932..52487448,15	MCF-7	breast:
33	chr20:52350699..52352639-chr20:52486021..52487199,7	MCF-7	breast:
34	chr20:52401623..52403995-chr20:52486040..52487259,28	MCF-7	breast:
35	chr20:52486286..52488897-chr20:55826084..55828899,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235415	Chromatin interaction
ENSG00000241721	Chromatin interaction
ENSG00000225563	Chromatin interaction
ENSG00000267064	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000126756	Chromatin interaction
ENSG00000259146	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000197555	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16998499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16998502	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16998533	1.00[EUR][1000 genomes]
rs57886257	1.00[EUR][1000 genomes]
rs59046998	1.00[EUR][1000 genomes]
rs6022721	1.00[AMR][1000 genomes]
rs7262342	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73275816	1.00[EUR][1000 genomes]
rs73275820	1.00[EUR][1000 genomes]
rs73914417	1.00[EUR][1000 genomes]
rs73914419	1.00[EUR][1000 genomes]
rs73914429	1.00[EUR][1000 genomes]
rs73914430	1.00[EUR][1000 genomes]
rs73914434	1.00[EUR][1000 genomes]
rs8114189	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	nsv586222	chr20:52473679-52506380	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	74 gene(s)	inside rSNPs	diseases
7	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
8	esv3403644	chr20:52484570-52487118	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52481800-52489200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52482800-52489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr20:52482800-52489400	Weak transcription	Aorta	Aorta
4	chr20:52482800-52489800	Weak transcription	Esophagus	oesophagus
5	chr20:52482800-52492000	Weak transcription	Gastric	stomach
6	chr20:52483400-52489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
8	chr20:52483600-52490600	Weak transcription	Right Atrium	heart
9	chr20:52483800-52488200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr20:52483800-52488600	Weak transcription	NHLF	lung
11	chr20:52484000-52488000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:52484000-52488800	Weak transcription	HSMMtube	muscle
13	chr20:52484200-52488800	Weak transcription	Fetal Stomach	stomach
14	chr20:52484400-52488800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:52484400-52488800	Weak transcription	Brain Hippocampus Middle	brain
16	chr20:52484600-52488400	Weak transcription	Brain Germinal Matrix	brain
17	chr20:52484800-52488000	Weak transcription	Fetal Brain Female	brain
18	chr20:52484800-52488200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:52484800-52488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:52484800-52488400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:52484800-52489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr20:52485000-52489200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr20:52485000-52489800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:52485000-52493000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:52485600-52487200	Enhancers	Placenta	Placenta
26	chr20:52485600-52487400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:52485600-52487600	Enhancers	Primary B cells from peripheral blood	blood
28	chr20:52485600-52489000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr20:52485600-52490400	Enhancers	Fetal Thymus	thymus
30	chr20:52485800-52487200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr20:52485800-52487200	Enhancers	Colonic Mucosa	Colon
32	chr20:52485800-52487600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr20:52485800-52487600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:52485800-52488600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr20:52485800-52489000	Enhancers	Liver	Liver
36	chr20:52485800-52489600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr20:52485800-52490200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr20:52485800-52490400	Enhancers	Fetal Intestine Small	intestine
39	chr20:52485800-52491000	Enhancers	Fetal Intestine Large	intestine
40	chr20:52486000-52487200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr20:52486000-52487200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:52486000-52487200	Enhancers	HMEC	breast
43	chr20:52486000-52487400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr20:52486000-52487400	Enhancers	Stomach Mucosa	stomach
45	chr20:52486000-52487800	Flanking Active TSS	HepG2	liver
46	chr20:52486000-52488400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:52486000-52488400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr20:52486000-52488800	Enhancers	Primary T cells from cord blood	blood
49	chr20:52486000-52488800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr20:52486000-52489000	Enhancers	Primary T helper cells fromperipheralblood	blood

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