Variant report

Variant	rs59358893
Chromosome Location	chr20:52534207-52534208
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52530267..52534413-chr20:55825060..55827185,3	MCF-7	breast:
2	chr20:52532038..52534829-chr6:88258936..88261704,2	MCF-7	breast:
3	chr20:52484799..52486540-chr20:52532724..52534997,2	K562	blood:
4	chr20:52532602..52534914-chr20:55844539..55846886,2	MCF-7	breast:
5	chr20:52533990..52535559-chr20:52546106..52547721,2	K562	blood:
6	chr20:52532392..52535656-chr20:52545674..52551256,6	K562	blood:
7	chr17:56736629..56738423-chr20:52533868..52536349,2	MCF-7	breast:
8	chr20:52367336..52371354-chr20:52530304..52536216,9	K562	blood:
9	chr20:52191644..52193527-chr20:52531481..52534421,2	K562	blood:
10	chr20:52531111..52535135-chr20:55839386..55843893,7	MCF-7	breast:
11	chr20:52530031..52532496-chr20:52533995..52537242,3	K562	blood:
12	chr20:52527549..52536399-chr20:55835927..55843462,13	MCF-7	breast:
13	chr20:52534131..52535812-chr20:52537419..52539689,2	K562	blood:
14	chr20:52531219..52535631-chr20:52536597..52539689,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs73275827	0.86[AFR][1000 genomes]
rs73275830	1.00[AMR][1000 genomes]
rs73914427	1.00[AMR][1000 genomes]
rs73914429	1.00[AMR][1000 genomes]
rs73914430	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52530000-52534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52532400-52534400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr20:52532400-52534800	Enhancers	Fetal Heart	heart
4	chr20:52532400-52534800	Enhancers	HMEC	breast
5	chr20:52532400-52534800	Enhancers	HSMMtube	muscle
6	chr20:52532400-52537400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52532400-52538400	Weak transcription	Esophagus	oesophagus
8	chr20:52532400-52542600	Weak transcription	Gastric	stomach
9	chr20:52532600-52534400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:52532600-52534400	Enhancers	Primary B cells from peripheral blood	blood
11	chr20:52532600-52534400	Enhancers	Right Atrium	heart
12	chr20:52532600-52534400	Enhancers	Right Ventricle	heart
13	chr20:52532600-52534600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:52532600-52534600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr20:52532600-52534800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:52532600-52534800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr20:52532600-52534800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr20:52532600-52534800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:52532600-52534800	Enhancers	Colon Smooth Muscle	Colon
20	chr20:52532600-52534800	Enhancers	Fetal Muscle Leg	muscle
21	chr20:52532600-52534800	Enhancers	Fetal Stomach	stomach
22	chr20:52532600-52535000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr20:52532600-52535000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr20:52532600-52535000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr20:52532600-52535200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:52532600-52535200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr20:52532600-52535200	Enhancers	Placenta	Placenta
28	chr20:52532600-52535800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr20:52532600-52535800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr20:52532600-52538400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr20:52532800-52534600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr20:52532800-52534600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr20:52532800-52534600	Enhancers	Fetal Lung	lung
34	chr20:52532800-52534800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr20:52532800-52534800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr20:52532800-52535600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr20:52533000-52534400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr20:52533000-52534400	Enhancers	Primary hematopoietic stem cells	blood
39	chr20:52533000-52534400	Enhancers	Brain Angular Gyrus	brain
40	chr20:52533000-52534400	Enhancers	Brain Anterior Caudate	brain
41	chr20:52533000-52534400	Enhancers	Brain Cingulate Gyrus	brain
42	chr20:52533000-52534400	Enhancers	Brain Hippocampus Middle	brain
43	chr20:52533000-52534400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr20:52533000-52534400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr20:52533000-52534400	Enhancers	Brain Substantia Nigra	brain
46	chr20:52533000-52534400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr20:52533000-52534600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr20:52533000-52534600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:52533000-52534600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr20:52533000-52534600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links