Variant report

Variant	rs6023458
Chromosome Location	chr20:53263210-53263211
allele	A/T
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:50)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52713087..52714018-chr20:53262887..53264220,11	MCF-7	breast:
2	chr20:52815887..52817150-chr20:53263089..53264049,8	MCF-7	breast:
3	chr20:53131931..53132565-chr20:53263125..53264081,2	MCF-7	breast:
4	chr20:52825609..52826186-chr20:53263084..53263835,2	MCF-7	breast:
5	chr20:52713364..52715301-chr20:53263047..53264602,2	MCF-7	breast:
6	chr20:53261472..53263254-chr3:64489100..64492065,2	MCF-7	breast:
7	chr20:52815188..52820648-chr20:53259065..53265987,10	MCF-7	breast:
8	chr20:52935516..52937390-chr20:53262812..53265904,3	MCF-7	breast:
9	chr20:52675939..52678149-chr20:53262263..53264864,2	MCF-7	breast:
10	chr17:59713376..59713904-chr20:53262989..53263725,2	MCF-7	breast:
11	chr20:53073220..53074160-chr20:53262587..53263752,7	MCF-7	breast:
12	chr20:53095482..53097034-chr20:53262598..53264162,9	MCF-7	breast:
13	chr20:53254267..53257182-chr20:53259848..53265627,6	MCF-7	breast:
14	chr20:53263118..53263726-chr8:134960043..134960857,2	MCF-7	breast:
15	chr20:52815942..52818202-chr20:53262668..53264663,9	MCF-7	breast:
16	chr20:52823570..52824812-chr20:53263070..53264046,10	MCF-7	breast:
17	chr20:52813822..52828208-chr20:53257867..53268573,36	MCF-7	breast:
18	chr20:52852339..52854018-chr20:53262598..53264931,2	MCF-7	breast:
19	chr20:52814485..52815216-chr20:53263065..53264324,5	MCF-7	breast:
20	chr20:52810712..52813833-chr20:53262210..53265088,4	MCF-7	breast:
21	chr20:52984992..52985954-chr20:53263110..53264230,3	MCF-7	breast:
22	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
23	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
24	chr20:53073207..53074105-chr20:53262668..53263905,3	MCF-7	breast:
25	chr20:52834958..52838732-chr20:53262770..53264255,82	MCF-7	breast:
26	chr20:47521695..47522213-chr20:53263102..53263773,2	MCF-7	breast:
27	chr20:53095947..53096812-chr20:53262655..53264011,3	MCF-7	breast:
28	chr20:52678948..52679961-chr20:53262987..53263883,4	MCF-7	breast:
29	chr20:52780969..52783846-chr20:53260965..53263576,2	MCF-7	breast:
30	chr20:52719607..52720196-chr20:53263139..53264090,2	K562	blood:
31	chr20:53071874..53072868-chr20:53263194..53264082,2	MCF-7	breast:
32	chr1:150951796..150952519-chr20:53263209..53263715,2	MCF-7	breast:
33	chr20:45824744..45825453-chr20:53262989..53263969,2	MCF-7	breast:
34	chr20:52835324..52837419-chr20:53262103..53264598,40	MCF-7	breast:
35	chr20:53262977..53263766-chr21:39542803..39543506,2	MCF-7	breast:
36	chr20:53145472..53146072-chr20:53263191..53264092,2	MCF-7	breast:
37	chr20:52684308..52686791-chr20:53262542..53265361,3	MCF-7	breast:
38	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
39	chr20:52889290..52890241-chr20:53263132..53264016,3	MCF-7	breast:
40	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:
41	chr20:52845491..52846135-chr20:53263111..53263838,3	MCF-7	breast:
42	chr20:52719655..52720664-chr20:53263098..53264661,7	MCF-7	breast:
43	chr15:99395963..99397912-chr20:53262204..53264774,2	MCF-7	breast:
44	chr20:52719704..52720659-chr20:53262955..53264259,5	MCF-7	breast:
45	chr20:52711973..52715362-chr20:53262880..53265739,4	MCF-7	breast:
46	chr20:53145937..53146842-chr20:53263038..53263918,2	MCF-7	breast:
47	chr20:53261648..53263825-chrX:153597457..153600320,2	MCF-7	breast:
48	chr20:52712940..52713980-chr20:53263049..53263631,3	K562	blood:
49	chr20:53263133..53263665-chr20:53284817..53285627,3	MCF-7	breast:
50	chr20:53261915..53264807-chr20:53286541..53288254,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000019186	Chromatin interaction
ENSG00000265595	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2904388	0.81[AMR][1000 genomes]
rs4811515	0.82[EUR][1000 genomes]
rs6014106	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6014107	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6014108	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6023457	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs910850	0.81[AMR][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:14 , 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	chr20:53260200-53264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:53260400-53266200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:53260800-53265200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:53260800-53266200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:53260800-53266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:53260800-53266200	Weak transcription	NH-A	brain
9	chr20:53260800-53266200	Weak transcription	NHDF-Ad	bronchial
10	chr20:53260800-53266200	Weak transcription	NHLF	lung
11	chr20:53260800-53266200	Weak transcription	Osteobl	bone
12	chr20:53262000-53263400	Enhancers	Fetal Brain Female	brain
13	chr20:53262200-53263600	Enhancers	Liver	Liver
14	chr20:53262400-53263800	Enhancers	Fetal Brain Male	brain

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