Variant report

Variant	rs2904388
Chromosome Location	chr20:53266697-53266698
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52813240..52815097-chr20:53265630..53268256,2	MCF-7	breast:
2	chr20:53265397..53266815-chr3:64515824..64517084,18	MCF-7	breast:
3	chr20:53265522..53267786-chr20:53285191..53286958,2	MCF-7	breast:
4	chr20:52874919..52877914-chr20:53265478..53267845,2	MCF-7	breast:
5	chr17:57919264..57921259-chr20:53265122..53266813,2	MCF-7	breast:
6	chr17:56708822..56710421-chr20:53264442..53267124,3	MCF-7	breast:
7	chr20:53091663..53093567-chr20:53264705..53266929,2	MCF-7	breast:
8	chr20:52813822..52828208-chr20:53257867..53268573,36	MCF-7	breast:
9	chr17:56734864..56737981-chr20:53266638..53268279,3	MCF-7	breast:
10	chr20:53266052..53267809-chr3:64513514..64515079,2	MCF-7	breast:
11	chr17:62398813..62401406-chr20:53265428..53267653,2	MCF-7	breast:
12	chr20:53265169..53266718-chr3:64518411..64520297,31	MCF-7	breast:
13	chr20:53264426..53266881-chr20:53274273..53275834,2	MCF-7	breast:
14	chr20:52882722..52884267-chr20:53265302..53267025,2	MCF-7	breast:
15	chr20:53263266..53270310-chr20:53278109..53284478,8	MCF-7	breast:
16	chr20:53265389..53267623-chr20:53296471..53298044,17	MCF-7	breast:
17	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
18	chr20:53265683..53266760-chr20:53284578..53285846,10	MCF-7	breast:
19	chr20:53265255..53267860-chr3:64509597..64511868,2	MCF-7	breast:
20	chr20:53265628..53267769-chr20:53342567..53344182,16	MCF-7	breast:
21	chr20:53266049..53266702-chr9:132647550..132648524,2	MCF-7	breast:
22	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
23	chr20:53264760..53267099-chr20:53297639..53299981,2	MCF-7	breast:
24	chr20:53264816..53267963-chr3:64518109..64521238,5	MCF-7	breast:
25	chr20:52685816..52688703-chr20:53265185..53266760,2	MCF-7	breast:
26	chr20:52720086..52722033-chr20:53263584..53267279,3	MCF-7	breast:
27	chr20:52676834..52679503-chr20:53266669..53268779,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000163638	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000101134	Chromatin interaction
ENSG00000101132	Chromatin interaction

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

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

rs_ID	r²[population]
rs1569985	0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1983702	0.86[GIH][hapmap]
rs2180462	0.91[GIH][hapmap]
rs4302265	0.80[GIH][hapmap]
rs4334548	0.91[GIH][hapmap]
rs4811515	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5024848	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6014106	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6014107	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6014108	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6023458	0.81[AMR][1000 genomes]
rs910849	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs910850	0.81[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[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:23 , 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	chr20:53265600-53267000	Enhancers	Fetal Brain Female	brain
3	chr20:53265800-53268200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr20:53266000-53268200	Enhancers	Brain Germinal Matrix	brain
5	chr20:53266200-53266800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:53266200-53266800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr20:53266200-53266800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:53266200-53266800	Enhancers	Brain Hippocampus Middle	brain
9	chr20:53266200-53267000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr20:53266200-53267000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr20:53266200-53267000	Enhancers	Brain Angular Gyrus	brain
12	chr20:53266200-53267200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:53266200-53267200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr20:53266200-53267200	Enhancers	Fetal Brain Male	brain
15	chr20:53266200-53267200	Enhancers	NH-A	brain
16	chr20:53266200-53267400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:53266200-53267400	Enhancers	Osteobl	bone
18	chr20:53266200-53267600	Enhancers	NHDF-Ad	bronchial
19	chr20:53266200-53267800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:53266200-53267800	Enhancers	NHLF	lung
21	chr20:53266200-53268000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:53266200-53269000	Enhancers	Fetal Lung	lung
23	chr20:53266200-53270800	Weak transcription	Ovary	ovary

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