Variant report

Variant	rs6083734
Chromosome Location	chr20:25057698-25057699
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25046045..25046980-chr20:25057133..25058078,4	MCF-7	breast:
2	chr20:25052320..25053946-chr20:25055898..25058573,2	MCF-7	breast:
3	chr20:25056370..25059250-chr20:25174569..25177571,3	MCF-7	breast:
4	chr20:25057289..25058975-chr20:25226619..25228863,2	MCF-7	breast:
5	chr20:25057340..25057881-chr20:25159450..25160139,2	MCF-7	breast:
6	chr20:25054844..25058216-chr20:25060336..25062971,3	MCF-7	breast:
7	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:
8	chr20:24975245..24975855-chr20:25057445..25058085,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction
ENSG00000100994	Chromatin interaction
ENSG00000100987	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2144372	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2207632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2387577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4815368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037013	1.00[JPT][hapmap]
rs6037014	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6083736	1.00[ASN][1000 genomes]
rs6083737	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6115024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115037	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304082	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	1.00[ASN][1000 genomes]
rs62217196	1.00[ASN][1000 genomes]
rs62217197	1.00[ASN][1000 genomes]
rs62217199	1.00[ASN][1000 genomes]
rs7263632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7266451	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7344824	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	1.00[ASN][1000 genomes]
rs761720	1.00[CHB][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	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25046800-25058200	Weak transcription	Right Atrium	heart
2	chr20:25056800-25058200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr20:25056800-25058600	Enhancers	Gastric	stomach
4	chr20:25057200-25058000	Enhancers	Hela-S3	cervix
5	chr20:25057200-25058200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:25057200-25058200	Enhancers	Liver	Liver
7	chr20:25057200-25058200	Enhancers	Pancreas	Pancrea
8	chr20:25057200-25058200	Enhancers	HMEC	breast
9	chr20:25057200-25058200	Bivalent Enhancer	NHEK	skin
10	chr20:25057200-25058400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr20:25057200-25058800	Bivalent Enhancer	Thymus	Thymus
12	chr20:25057200-25060600	Enhancers	Dnd41	blood
13	chr20:25057400-25057800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr20:25057400-25057800	Bivalent Enhancer	NHDF-Ad	bronchial
15	chr20:25057400-25058000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr20:25057400-25058000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr20:25057400-25058000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:25057400-25058000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:25057400-25058000	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr20:25057400-25058000	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr20:25057400-25058000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
22	chr20:25057400-25058000	Bivalent Enhancer	HepG2	liver
23	chr20:25057400-25058200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:25057400-25058200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:25057400-25058200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:25057400-25058200	Bivalent Enhancer	Left Ventricle	heart
27	chr20:25057400-25058200	Flanking Active TSS	A549	lung
28	chr20:25057400-25058400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr20:25057400-25058400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
30	chr20:25057400-25058600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
31	chr20:25057400-25058800	Enhancers	Placenta	Placenta
32	chr20:25057600-25057800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:25057600-25057800	Enhancers	Brain Angular Gyrus	brain
34	chr20:25057600-25057800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
35	chr20:25057600-25057800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:25057600-25058000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr20:25057600-25058000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25057600-25058000	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr20:25057600-25058000	Weak transcription	Esophagus	oesophagus
40	chr20:25057600-25058000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
41	chr20:25057600-25058000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
42	chr20:25057600-25058200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr20:25057600-25058200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
44	chr20:25057600-25058200	Bivalent Enhancer	Osteobl	bone
45	chr20:25057600-25058400	Bivalent Enhancer	Stomach Mucosa	stomach
46	chr20:25057600-25058800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr20:25057600-25059000	Active TSS	Brain Inferior Temporal Lobe	brain

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