Variant report

Variant	rs873078
Chromosome Location	chr20:53260343-53260344
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:53258691..53260820-chr9:131702974..131705008,2	MCF-7	breast:
2	chr20:52815188..52820648-chr20:53259065..53265987,10	MCF-7	breast:
3	chr17:56708372..56710185-chr20:53258273..53260843,2	MCF-7	breast:
4	chr20:53254267..53257182-chr20:53259848..53265627,6	MCF-7	breast:
5	chr20:53212410..53215334-chr20:53259205..53262055,2	MCF-7	breast:
6	chr20:52813822..52828208-chr20:53257867..53268573,36	MCF-7	breast:
7	chr20:53184299..53185930-chr20:53258738..53260954,2	K562	blood:
8	chr20:52836143..52836746-chr20:53260129..53260690,2	MCF-7	breast:
9	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
10	chr20:52746822..52749791-chr20:53258985..53261806,2	MCF-7	breast:
11	chr20:53257490..53260450-chr3:64522164..64524068,2	MCF-7	breast:
12	chr20:53240556..53242975-chr20:53260288..53262063,2	MCF-7	breast:
13	chr20:52681034..52683636-chr20:53260094..53262163,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000251184	Chromatin interaction

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

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

rs_ID	r²[population]
rs10485784	1.00[GIH][hapmap]
rs35437239	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55645278	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6014059	1.00[GIH][hapmap]
rs6023251	1.00[GIH][hapmap]
rs6023383	1.00[GIH][hapmap]
rs6023456	0.82[EUR][1000 genomes]
rs6064098	0.90[YRI][hapmap]
rs6068930	1.00[GIH][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs6091886	1.00[GIH][hapmap]
rs6098099	1.00[GIH][hapmap]
rs6098118	1.00[GIH][hapmap]

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	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
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:53257600-53266000	Weak transcription	Brain Germinal Matrix	brain
3	chr20:53259200-53260600	Enhancers	Fetal Muscle Leg	muscle
4	chr20:53259400-53260800	Enhancers	NHDF-Ad	bronchial
5	chr20:53259600-53260400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:53259600-53260800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:53259600-53260800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:53259600-53260800	Enhancers	Fetal Brain Male	brain
9	chr20:53259600-53260800	Enhancers	NH-A	brain
10	chr20:53259800-53260800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:53259800-53260800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:53259800-53260800	Enhancers	NHLF	lung
13	chr20:53260000-53260400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr20:53260000-53260600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:53260000-53260600	Genic enhancers	Fetal Brain Female	brain
16	chr20:53260000-53260800	Enhancers	Pancreas	Pancrea
17	chr20:53260000-53260800	Flanking Active TSS	Osteobl	bone
18	chr20:53260200-53260400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:53260200-53260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:53260200-53260800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:53260200-53260800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr20:53260200-53264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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