Variant report

Variant	rs6064100
Chromosome Location	chr20:53265636-53265637
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:43)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:43 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52813240..52815097-chr20:53265630..53268256,2	MCF-7	breast:
2	chr20:53265198..53266621-chr20:53273417..53274330,6	MCF-7	breast:
3	chr20:52815188..52820648-chr20:53259065..53265987,10	MCF-7	breast:
4	chr20:53265397..53266815-chr3:64515824..64517084,18	MCF-7	breast:
5	chr20:53265522..53267786-chr20:53285191..53286958,2	MCF-7	breast:
6	chr20:52935516..52937390-chr20:53262812..53265904,3	MCF-7	breast:
7	chr20:52885262..52886034-chr20:53264976..53265669,2	MCF-7	breast:
8	chr20:52874919..52877914-chr20:53265478..53267845,2	MCF-7	breast:
9	chr17:57919264..57921259-chr20:53265122..53266813,2	MCF-7	breast:
10	chr17:56708822..56710421-chr20:53264442..53267124,3	MCF-7	breast:
11	chr20:52825697..52826381-chr20:53265099..53266098,2	MCF-7	breast:
12	chr20:53091663..53093567-chr20:53264705..53266929,2	MCF-7	breast:
13	chr20:52813822..52828208-chr20:53257867..53268573,36	MCF-7	breast:
14	chr20:52836035..52837008-chr20:53264640..53266086,4	MCF-7	breast:
15	chr20:46304685..46305250-chr20:53265630..53266203,2	MCF-7	breast:
16	chr20:53094262..53095242-chr20:53265441..53266262,2	MCF-7	breast:
17	chr17:62398813..62401406-chr20:53265428..53267653,2	MCF-7	breast:
18	chr17:56708493..56710309-chr20:53263486..53265708,2	MCF-7	breast:
19	chr20:53265169..53266718-chr3:64518411..64520297,31	MCF-7	breast:
20	chr20:53264426..53266881-chr20:53274273..53275834,2	MCF-7	breast:
21	chr20:52882722..52884267-chr20:53265302..53267025,2	MCF-7	breast:
22	chr20:53263266..53270310-chr20:53278109..53284478,8	MCF-7	breast:
23	chr20:53265389..53267623-chr20:53296471..53298044,17	MCF-7	breast:
24	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
25	chr20:53265357..53266518-chr3:64703553..64704483,6	MCF-7	breast:
26	chr20:53095873..53096821-chr20:53265191..53266014,2	MCF-7	breast:
27	chr20:53264843..53266677-chr20:53266709..53268595,2	MCF-7	breast:
28	chr20:52556204..52556803-chr20:53265004..53266186,3	MCF-7	breast:
29	chr20:53265591..53266241-chr3:64008970..64009620,2	MCF-7	breast:
30	chr20:53265556..53266634-chr3:64015951..64016993,5	MCF-7	breast:
31	chr20:53265255..53267860-chr3:64509597..64511868,2	MCF-7	breast:
32	chr20:53265628..53267769-chr20:53342567..53344182,16	MCF-7	breast:
33	chr20:53218462..53220917-chr20:53263377..53265971,2	MCF-7	breast:
34	chr20:52823877..52824684-chr20:53265592..53266220,2	MCF-7	breast:
35	chr20:53265608..53266631-chr20:54756045..54757184,3	MCF-7	breast:
36	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
37	chr20:53264760..53267099-chr20:53297639..53299981,2	MCF-7	breast:
38	chr20:52711973..52715362-chr20:53262880..53265739,4	MCF-7	breast:
39	chr20:53264816..53267963-chr3:64518109..64521238,5	MCF-7	breast:
40	chr20:52685816..52688703-chr20:53265185..53266760,2	MCF-7	breast:
41	chr20:52720086..52722033-chr20:53263584..53267279,3	MCF-7	breast:
42	chr20:53265482..53266585-chr3:64515878..64516670,6	MCF-7	breast:
43	chr20:53073193..53074159-chr20:53265077..53266051,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163636	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000101134	Chromatin interaction
ENSG00000163638	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000064787	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1569982	0.90[AMR][1000 genomes]
rs1569983	0.90[AMR][1000 genomes]
rs1569984	0.90[AMR][1000 genomes]
rs1983702	0.83[AMR][1000 genomes]
rs2180462	0.93[AMR][1000 genomes]
rs4302265	0.93[AMR][1000 genomes]
rs4334548	0.93[AMR][1000 genomes]
rs4811514	0.83[AMR][1000 genomes]
rs6014103	0.93[AMR][1000 genomes]
rs6014105	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6023441	0.93[AMR][1000 genomes]
rs6023451	0.93[AMR][1000 genomes]
rs6068929	0.95[AMR][1000 genomes];0.81[EUR][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	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:13 , 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	chr20:53260400-53266200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:53260800-53266200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:53260800-53266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr20:53260800-53266200	Weak transcription	NH-A	brain
7	chr20:53260800-53266200	Weak transcription	NHDF-Ad	bronchial
8	chr20:53260800-53266200	Weak transcription	NHLF	lung
9	chr20:53260800-53266200	Weak transcription	Osteobl	bone
10	chr20:53263800-53266200	Weak transcription	Fetal Brain Male	brain
11	chr20:53264400-53266400	Enhancers	Placenta	Placenta
12	chr20:53265200-53266000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:53265600-53267000	Enhancers	Fetal Brain Female	brain

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