Variant report

Variant	rs28406117
Chromosome Location	chr20:52976479-52976480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1014808	0.82[ASN][1000 genomes]
rs1407043	0.86[ASN][1000 genomes]
rs16999597	0.84[ASN][1000 genomes]
rs1841860	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1923118	0.85[ASN][1000 genomes]
rs2126676	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28429972	0.99[ASN][1000 genomes]
rs56881371	0.96[ASN][1000 genomes]
rs59924072	0.99[ASN][1000 genomes]
rs6013987	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013989	0.98[ASN][1000 genomes]
rs6013997	0.86[ASN][1000 genomes]
rs6013999	0.85[ASN][1000 genomes]
rs6014003	0.85[ASN][1000 genomes]
rs6014004	0.83[ASN][1000 genomes]
rs6014005	0.84[ASN][1000 genomes]
rs6023153	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023154	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023155	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6023156	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6023158	0.94[ASN][1000 genomes]
rs6023163	0.99[ASN][1000 genomes]
rs6023164	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023178	0.83[ASN][1000 genomes]
rs6023179	0.83[ASN][1000 genomes]
rs6023180	0.87[ASN][1000 genomes]
rs6023181	0.83[ASN][1000 genomes]
rs6023185	0.83[ASN][1000 genomes]
rs6023189	0.85[ASN][1000 genomes]
rs6023192	0.84[ASN][1000 genomes]
rs6023193	0.84[ASN][1000 genomes]
rs6023203	0.85[ASN][1000 genomes]
rs6091856	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097934	0.95[ASN][1000 genomes]
rs6097938	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097939	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097940	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097941	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097945	0.96[ASN][1000 genomes]
rs6097946	0.96[ASN][1000 genomes]
rs6097963	0.84[ASN][1000 genomes]
rs73624107	1.00[ASN][1000 genomes]
rs73624108	0.99[ASN][1000 genomes]
rs73624110	0.99[ASN][1000 genomes]
rs793033	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52972600-52977600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:52974000-52977800	Weak transcription	Fetal Brain Female	brain
3	chr20:52974000-52978200	Weak transcription	Ovary	ovary
4	chr20:52975000-52977400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:52976000-52976600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr20:52976000-52978400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:52976200-52976600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr20:52976200-52976600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr20:52976200-52977600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr20:52976200-52977800	Enhancers	HUES48 Cell Line	embryonic stem cell

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