Variant report

Variant	rs208642
Chromosome Location	chr20:52631859-52631860
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:204256116..204257768-chr20:52629931..52632610,2	MCF-7	breast:
2	chr17:58822624..58823604-chr20:52631281..52631868,2	MCF-7	breast:
3	chr17:58821313..58822027-chr20:52631455..52632491,3	MCF-7	breast:
4	chr17:58822484..58823239-chr20:52631304..52631920,2	MCF-7	breast:
5	chr12:89857154..89857707-chr20:52631451..52632053,2	MCF-7	breast:
6	chr17:58822640..58823282-chr20:52631303..52632583,5	MCF-7	breast:
7	chr17:58821413..58822386-chr20:52630813..52631902,3	MCF-7	breast:
8	chr17:58820431..58822124-chr20:52629626..52633490,4	MCF-7	breast:
9	chr17:58820299..58823467-chr20:52630245..52633492,6	MCF-7	breast:

No data

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11699406	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs158539	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158541	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158546	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158549	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158550	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299720	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs290384	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290386	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290388	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290390	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290417	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290421	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290453	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290456	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290457	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290458	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290459	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290462	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290466	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290471	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378782	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71623	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52624000-52633400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:52627600-52633200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52630200-52632200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52630600-52632200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr20:52630800-52633200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52631000-52633200	Weak transcription	Brain Substantia Nigra	brain
9	chr20:52631200-52632200	Enhancers	GM12878-XiMat	blood
10	chr20:52631400-52633000	Weak transcription	Brain Anterior Caudate	brain
11	chr20:52631400-52634400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:52631400-52635800	Weak transcription	Stomach Mucosa	stomach
13	chr20:52631400-52637000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr20:52631600-52632000	Weak transcription	Brain Hippocampus Middle	brain
16	chr20:52631600-52632200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:52631600-52633400	Weak transcription	Adipose Nuclei	Adipose
18	chr20:52631600-52634600	Weak transcription	Fetal Lung	lung
19	chr20:52631600-52636000	Weak transcription	NHDF-Ad	bronchial

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