Variant report

Variant	rs2299727
Chromosome Location	chr20:52596793-52596794
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52596205..52597011-chr20:52765364..52765924,2	MCF-7	breast:
2	chr10:63845311..63847924-chr20:52594546..52597386,2	MCF-7	breast:
3	chr20:52596286..52597038-chr20:52811502..52812174,4	MCF-7	breast:
4	chr20:52596286..52596804-chr20:52811617..52812118,2	MCF-7	breast:
5	chr17:56716851..56717594-chr20:52596237..52597195,2	MCF-7	breast:
6	chr1:41067796..41070793-chr20:52595128..52597334,3	MCF-7	breast:
7	chr20:52596227..52596815-chr20:52739956..52740669,2	MCF-7	breast:
8	chr20:52595597..52599294-chr20:52683836..52687749,4	MCF-7	breast:
9	chr20:52594177..52596911-chr20:52824324..52827148,2	MCF-7	breast:
10	chr20:52596289..52597066-chr20:52740123..52740715,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000064787	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1034843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs158544	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208364	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs208372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208375	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276492	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276508	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2276511	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299733	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2299736	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290389	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs290424	0.83[AMR][1000 genomes]
rs290425	0.83[AMR][1000 genomes]
rs290426	0.83[AMR][1000 genomes]
rs36030456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs406691	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs459454	0.83[AMR][1000 genomes]
rs4809948	0.88[ASN][1000 genomes]
rs4811488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6091791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6091792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091796	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6091799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6097693	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097694	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097695	0.90[ASN][1000 genomes]
rs6097696	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6097697	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52580800-52600000	Weak transcription	Stomach Mucosa	stomach
3	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52591200-52597000	Strong transcription	HSMMtube	muscle
5	chr20:52592000-52599600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52592800-52599600	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:52593000-52600800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52593200-52601000	Weak transcription	Brain Substantia Nigra	brain
9	chr20:52596000-52597400	Enhancers	Fetal Lung	lung
10	chr20:52596000-52597600	Enhancers	Fetal Stomach	stomach
11	chr20:52596200-52597200	Weak transcription	Placenta	Placenta
12	chr20:52596400-52601400	Weak transcription	Rectal Mucosa Donor 31	rectum

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