Variant report

Variant	rs57886257
Chromosome Location	chr20:52551434-52551435
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52194896..52195863-chr20:52550123..52551759,4	MCF-7	breast:
2	chr20:52367670..52370398-chr20:52548161..52552939,6	K562	blood:
3	chr20:52548636..52551590-chr20:52814166..52816550,2	MCF-7	breast:
4	chr20:52521138..52522738-chr20:52550916..52552554,2	K562	blood:
5	chr17:57109264..57111051-chr20:52551167..52554043,2	MCF-7	breast:
6	chr20:52469682..52472418-chr20:52551027..52553100,2	K562	blood:
7	chr20:52551078..52553567-chr20:55847607..55851332,6	MCF-7	breast:
8	chr17:57921749..57924885-chr20:52550467..52553589,3	MCF-7	breast:
9	chr20:52548692..52552101-chr20:55839394..55841994,3	MCF-7	breast:
10	chr20:52368056..52371228-chr20:52549159..52552395,4	K562	blood:
11	chr20:52203936..52206746-chr20:52550032..52552286,2	K562	blood:
12	chr20:52550372..52553297-chr20:52685903..52688143,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000064787	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16998499	1.00[EUR][1000 genomes]
rs16998502	1.00[EUR][1000 genomes]
rs16998533	1.00[EUR][1000 genomes]
rs58979406	1.00[EUR][1000 genomes]
rs59046998	1.00[EUR][1000 genomes]
rs7262342	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]
rs8114866	1.00[EUR][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	chr20:52538400-52553400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52543600-52556000	Weak transcription	Aorta	Aorta
3	chr20:52543800-52555000	Weak transcription	Stomach Mucosa	stomach
4	chr20:52544800-52552000	Weak transcription	Lung	lung
5	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:52549400-52553800	Enhancers	Primary hematopoietic stem cells	blood
7	chr20:52549800-52552600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr20:52550000-52551600	Enhancers	Colon Smooth Muscle	Colon
9	chr20:52550000-52552600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr20:52550000-52552600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr20:52550000-52552600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr20:52550000-52552600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr20:52550000-52552600	Enhancers	HUVEC	blood vessel
14	chr20:52550000-52552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:52550000-52552800	Enhancers	Primary T cells from cord blood	blood
16	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
17	chr20:52550200-52551600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr20:52550200-52552000	Flanking Active TSS	K562	blood
19	chr20:52550200-52552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr20:52550200-52552200	Enhancers	Fetal Stomach	stomach
21	chr20:52550200-52552200	Flanking Active TSS	GM12878-XiMat	blood
22	chr20:52550200-52552200	Enhancers	NHDF-Ad	bronchial
23	chr20:52550200-52552600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:52550200-52552600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr20:52550200-52552600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:52550200-52552600	Enhancers	Fetal Muscle Leg	muscle
27	chr20:52550200-52552600	Enhancers	Fetal Thymus	thymus
28	chr20:52550200-52553000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr20:52550200-52555000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:52550400-52551800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr20:52550400-52552200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:52550400-52552200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr20:52550400-52552600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr20:52550400-52552600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr20:52550400-52557400	Enhancers	Placenta	Placenta
36	chr20:52550600-52551600	Enhancers	Brain Hippocampus Middle	brain
37	chr20:52550600-52551600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr20:52550600-52551800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr20:52550600-52552200	Enhancers	Fetal Kidney	kidney
40	chr20:52550600-52552400	Enhancers	Fetal Lung	lung
41	chr20:52550600-52552400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr20:52550600-52552600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr20:52550600-52552600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr20:52550600-52552600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr20:52550600-52552600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr20:52550600-52552600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr20:52550600-52552600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr20:52550800-52551600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr20:52550800-52552000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr20:52550800-52552000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links