Variant report

Variant	rs7262342
Chromosome Location	chr20:52490308-52490309
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:58601420..58603983-chr20:52490138..52492332,2	MCF-7	breast:
2	chr20:52229223..52229752-chr20:52489669..52490388,2	MCF-7	breast:
3	chr17:57922823..57924749-chr20:52487976..52490735,3	MCF-7	breast:
4	chr17:57919005..57920769-chr20:52489404..52491830,2	MCF-7	breast:
5	chr20:49346871..49348978-chr20:52488484..52490974,2	MCF-7	breast:
6	chr20:52471901..52491673-chr20:55835708..55845674,34	MCF-7	breast:
7	chr20:52369283..52371652-chr20:52490163..52491937,2	K562	blood:
8	chr20:52488667..52491302-chr20:52499908..52502050,2	K562	blood:
9	chr1:144930770..144933506-chr20:52490207..52493077,2	MCF-7	breast:
10	chr20:52445950..52448025-chr20:52488646..52490930,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124171	Chromatin interaction
ENSG00000178104	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16998499	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16998502	0.99[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]
rs58979406	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59046998	1.00[EUR][1000 genomes]
rs6022721	1.00[AMR][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:7 , 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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52482800-52492000	Weak transcription	Gastric	stomach
2	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
3	chr20:52483600-52490600	Weak transcription	Right Atrium	heart
4	chr20:52485000-52493000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:52485600-52490400	Enhancers	Fetal Thymus	thymus
6	chr20:52485800-52490400	Enhancers	Fetal Intestine Small	intestine
7	chr20:52485800-52491000	Enhancers	Fetal Intestine Large	intestine
8	chr20:52486000-52490400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr20:52486000-52490400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr20:52486200-52490400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr20:52486200-52490400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr20:52487200-52490400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr20:52487400-52495000	Weak transcription	Small Intestine	intestine
14	chr20:52487400-52495400	Weak transcription	K562	blood
15	chr20:52488000-52490400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr20:52488200-52490400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr20:52488200-52490600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr20:52488800-52490400	Flanking Active TSS	GM12878-XiMat	blood
19	chr20:52489000-52491200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr20:52489000-52493200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr20:52489000-52494600	Weak transcription	Liver	Liver
22	chr20:52489200-52491800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr20:52489600-52491200	Enhancers	Primary B cells from cord blood	blood
24	chr20:52489800-52490600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:52489800-52490600	Enhancers	Primary B cells from peripheral blood	blood
26	chr20:52490000-52490400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:52490000-52490400	Enhancers	Dnd41	blood
28	chr20:52490000-52490800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr20:52490000-52491000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr20:52490000-52491000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:52490000-52491000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr20:52490000-52491400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr20:52490000-52494000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr20:52490000-52494400	Weak transcription	Fetal Kidney	kidney
35	chr20:52490000-52494800	Weak transcription	A549	lung
36	chr20:52490000-52495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr20:52490200-52490400	Enhancers	Primary T cells from cord blood	blood
38	chr20:52490200-52490400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr20:52490200-52490800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr20:52490200-52491000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr20:52490200-52491000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr20:52490200-52491000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr20:52490200-52491000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr20:52490200-52491400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr20:52490200-52491400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr20:52490200-52491800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr20:52490200-52491800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr20:52490200-52492000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr20:52490200-52492000	Weak transcription	Brain Germinal Matrix	brain
50	chr20:52490200-52493200	Weak transcription	H1 Cell Line	embryonic stem cell

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