Variant report

Variant	rs6023496
Chromosome Location	chr20:53297325-53297326
allele	C/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:53)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:53 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr20:53297245..53298058-chr3:64752403..64753296,2	MCF-7	breast:
2	chr1:61620670..61621170-chr20:53297255..53298211,4	MCF-7	breast:
3	chr20:53297140..53298069-chr20:54745859..54746826,6	MCF-7	breast:
4	chr20:53296558..53298632-chr3:64515452..64516902,29	MCF-7	breast:
5	chr17:56735402..56737734-chr20:53294537..53297494,2	MCF-7	breast:
6	chr20:46292237..46293076-chr20:53297070..53297816,2	MCF-7	breast:
7	chr20:53294274..53296254-chr20:53296968..53298496,2	MCF-7	breast:
8	chr20:46306630..46307190-chr20:53297136..53297960,2	MCF-7	breast:
9	chr20:52559737..52560546-chr20:53297221..53297991,3	MCF-7	breast:
10	chr20:46354084..46354697-chr20:53296998..53297657,2	MCF-7	breast:
11	chr20:53297153..53297931-chr3:64560929..64561796,3	MCF-7	breast:
12	chr20:53297176..53297814-chr3:62608129..62608650,2	MCF-7	breast:
13	chr20:53297155..53297942-chr8:108982967..108983686,2	MCF-7	breast:
14	chr20:53297039..53297648-chr3:64543662..64544449,2	MCF-7	breast:
15	chr20:52559479..52560840-chr20:53297067..53298188,6	MCF-7	breast:
16	chr18:38070773..38071274-chr20:53297047..53297663,2	MCF-7	breast:
17	chr17:62396854..62397477-chr20:53297283..53297991,2	MCF-7	breast:
18	chr20:53296906..53298947-chr20:53330986..53333656,2	MCF-7	breast:
19	chr20:53297180..53297923-chr21:9826146..9827023,2	MCF-7	breast:
20	chr20:53297100..53298020-chr20:54756384..54757317,8	MCF-7	breast:
21	chr1:61620670..61621170-chr20:53297146..53297782,3	MCF-7	breast:
22	chr17:62398179..62399057-chr20:53297171..53297878,3	MCF-7	breast:
23	chr20:53297077..53298037-chr3:64523265..64523990,2	MCF-7	breast:
24	chr20:53297044..53298391-chr20:53342876..53343999,9	MCF-7	breast:
25	chr20:53296415..53300428-chr3:64512136..64516086,4	MCF-7	breast:
26	chr20:53297264..53297860-chr20:53322089..53322721,2	MCF-7	breast:
27	chr20:53297064..53298077-chr3:64515896..64517016,10	MCF-7	breast:
28	chr20:53297072..53298027-chr20:54824104..54825055,3	K562	blood:
29	chr20:53297141..53300024-chr20:53303959..53305467,2	MCF-7	breast:
30	chr20:53295710..53298032-chr3:64518048..64519638,2	MCF-7	breast:
31	chr20:53297063..53298490-chr3:64703588..64704964,7	MCF-7	breast:
32	chr20:53296962..53298212-chr3:62618518..62619402,4	MCF-7	breast:
33	chr17:62391951..62394828-chr20:53295220..53297962,2	MCF-7	breast:
34	chr20:53297030..53299399-chr3:64518913..64520051,28	MCF-7	breast:
35	chr20:53296950..53299252-chr3:64517666..64520403,2	MCF-7	breast:
36	chr12:78539699..78540376-chr20:53297270..53297982,2	MCF-7	breast:
37	chr20:53297137..53297884-chr3:62608070..62608680,2	MCF-7	breast:
38	chr20:53284827..53285806-chr20:53297032..53297616,3	MCF-7	breast:
39	chr20:53297104..53297971-chr3:64671114..64672022,2	MCF-7	breast:
40	chr20:53296551..53298207-chr20:53342710..53343895,13	MCF-7	breast:
41	chr20:53265389..53267623-chr20:53296471..53298044,17	MCF-7	breast:
42	chr17:59651969..59652895-chr20:53297083..53297793,2	MCF-7	breast:
43	chr20:53287233..53287980-chr20:53296972..53297626,2	MCF-7	breast:
44	chr20:53296916..53298758-chr3:64518136..64520683,88	MCF-7	breast:
45	chr20:53293305..53299094-chr20:53306694..53312269,5	MCF-7	breast:
46	chr20:53290085..53292614-chr20:53295758..53297521,2	MCF-7	breast:
47	chr20:53297230..53298183-chr3:64015995..64017242,8	MCF-7	breast:
48	chr17:62397987..62399090-chr20:53297150..53298132,13	MCF-7	breast:
49	chr20:52556178..52557055-chr20:53297089..53298051,7	MCF-7	breast:
50	chr20:52556090..52556889-chr20:53296922..53298074,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000255438	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000264063	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000163638	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11905815	1.00[EUR][1000 genomes]
rs11905874	1.00[EUR][1000 genomes]
rs11906031	1.00[CEU][hapmap]
rs12479694	1.00[EUR][1000 genomes]
rs12479859	1.00[EUR][1000 genomes]
rs12480028	1.00[EUR][1000 genomes]
rs12480040	1.00[EUR][1000 genomes]
rs12480381	1.00[EUR][1000 genomes]
rs12480981	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12481217	1.00[EUR][1000 genomes]
rs12481344	1.00[EUR][1000 genomes]
rs12481541	1.00[EUR][1000 genomes]
rs16999798	1.00[CEU][hapmap]
rs16999810	1.00[CEU][hapmap]
rs2426524	1.00[CEU][hapmap]
rs35234783	1.00[EUR][1000 genomes]
rs6014109	1.00[EUR][1000 genomes]
rs6014129	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023417	1.00[CEU][hapmap]
rs6023465	1.00[EUR][1000 genomes]
rs6023487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023489	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6091940	1.00[CEU][hapmap]
rs6512974	1.00[CEU][hapmap]
rs6512975	1.00[CEU][hapmap]
rs6512981	1.00[CEU][hapmap]
rs7265834	1.00[CEU][hapmap]
rs7266570	1.00[EUR][1000 genomes]
rs7271008	1.00[CEU][hapmap]
rs7271632	1.00[CEU][hapmap]
rs73913649	1.00[EUR][1000 genomes]
rs8114817	1.00[CEU][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	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
2	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
3	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
4	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
5	nsv586283	chr20:53288595-53311415	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53296800-53299600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:53297000-53298200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:53297000-53298200	Enhancers	Colon Smooth Muscle	Colon
4	chr20:53297000-53298600	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr20:53297000-53299200	Enhancers	Brain Germinal Matrix	brain
6	chr20:53297200-53297400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr20:53297200-53297600	Enhancers	Liver	Liver
8	chr20:53297200-53297800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr20:53297200-53298200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr20:53297200-53298200	Enhancers	Rectal Smooth Muscle	rectum
11	chr20:53297200-53298600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:53297200-53298600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr20:53297200-53298800	Enhancers	Fetal Brain Female	brain
14	chr20:53297200-53299000	Enhancers	Stomach Smooth Muscle	stomach
15	chr20:53297200-53299600	Enhancers	Fetal Stomach	stomach

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