Variant report

Variant	rs59731128
Chromosome Location	chr20:25037810-25037811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25024429..25027041-chr20:25035643..25038257,2	K562	blood:
2	chr20:25026036..25030944-chr20:25033529..25038477,7	MCF-7	breast:
3	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
4	chr20:24993232..24996113-chr20:25036389..25038769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11904887	0.86[AFR][1000 genomes]
rs11908084	0.84[AFR][1000 genomes]
rs55879612	1.00[ASN][1000 genomes]
rs58083478	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25036600-25038000	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr20:25036600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr20:25036600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr20:25036800-25038200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr20:25036800-25038600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr20:25036800-25038600	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr20:25036800-25039200	Active TSS	Fetal Intestine Large	intestine
8	chr20:25037000-25038000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr20:25037000-25038000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr20:25037200-25038000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:25037200-25038000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr20:25037200-25038000	Flanking Active TSS	Fetal Muscle Trunk	muscle
13	chr20:25037200-25038400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr20:25037200-25038600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:25037200-25038800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:25037200-25039800	Active TSS	Aorta	Aorta
17	chr20:25037400-25038000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr20:25037400-25038000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr20:25037400-25038000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:25037400-25038000	Flanking Bivalent TSS/Enh	NHEK	skin
21	chr20:25037400-25038200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:25037400-25038600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr20:25037400-25038800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
24	chr20:25037400-25039200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:25037400-25039200	Active TSS	Brain Angular Gyrus	brain
26	chr20:25037400-25039200	Active TSS	Fetal Intestine Small	intestine
27	chr20:25037400-25039400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr20:25037400-25039600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr20:25037400-25039600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:25037400-25039600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr20:25037400-25039600	Active TSS	Ovary	ovary
32	chr20:25037400-25040200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr20:25037600-25038000	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:25037600-25038000	Active TSS	Brain Germinal Matrix	brain
35	chr20:25037600-25038000	Flanking Active TSS	Fetal Brain Female	brain
36	chr20:25037600-25038000	Flanking Active TSS	NH-A	brain
37	chr20:25037600-25038000	Flanking Active TSS	Osteobl	bone
38	chr20:25037600-25038200	Weak transcription	Fetal Heart	heart
39	chr20:25037600-25038400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:25037600-25038600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr20:25037600-25038600	Flanking Active TSS	HMEC	breast
42	chr20:25037600-25038600	Flanking Active TSS	HUVEC	blood vessel
43	chr20:25037600-25039000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:25037600-25039000	Active TSS	Primary T cells from cord blood	blood
45	chr20:25037600-25039000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr20:25037600-25039000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr20:25037600-25039000	Active TSS	Brain Cingulate Gyrus	brain
48	chr20:25037600-25039000	Active TSS	Brain Hippocampus Middle	brain
49	chr20:25037600-25039000	Active TSS	Stomach Mucosa	stomach
50	chr20:25037600-25039000	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links