Variant report

Variant	rs28429972
Chromosome Location	chr20:52985789-52985790
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:49347789..49349298-chr20:52984375..52987184,2	MCF-7	breast:
2	chr20:52984992..52985954-chr20:53263110..53264230,3	MCF-7	breast:
3	chr20:52983863..52986994-chr20:52995623..52998239,3	MCF-7	breast:
4	chr20:49347583..49351619-chr20:52982625..52987672,5	MCF-7	breast:
5	chr20:52983415..52985850-chr6:27858765..27861037,2	MCF-7	breast:
6	chr20:52982179..52987061-chr20:52989270..52993345,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000124171	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1014808	0.83[ASN][1000 genomes]
rs1407043	0.87[ASN][1000 genomes]
rs16999559	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16999597	0.85[ASN][1000 genomes]
rs1841860	0.91[ASN][1000 genomes]
rs1923118	0.86[ASN][1000 genomes]
rs2126676	0.90[ASN][1000 genomes]
rs28406117	0.99[ASN][1000 genomes]
rs56881371	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59924072	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013987	0.99[ASN][1000 genomes]
rs6013989	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6013997	0.87[ASN][1000 genomes]
rs6013999	0.86[ASN][1000 genomes]
rs6014003	0.86[ASN][1000 genomes]
rs6014004	0.85[ASN][1000 genomes]
rs6014005	0.85[ASN][1000 genomes]
rs6023153	0.95[ASN][1000 genomes]
rs6023154	0.95[ASN][1000 genomes]
rs6023155	0.96[ASN][1000 genomes]
rs6023156	0.96[ASN][1000 genomes]
rs6023158	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023163	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023164	1.00[ASN][1000 genomes]
rs6023178	0.84[ASN][1000 genomes]
rs6023179	0.84[ASN][1000 genomes]
rs6023180	0.89[ASN][1000 genomes]
rs6023181	0.84[ASN][1000 genomes]
rs6023185	0.84[ASN][1000 genomes]
rs6023189	0.87[ASN][1000 genomes]
rs6023192	0.85[ASN][1000 genomes]
rs6023193	0.85[ASN][1000 genomes]
rs6023203	0.86[ASN][1000 genomes]
rs6091856	0.92[ASN][1000 genomes]
rs6097934	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097938	0.90[ASN][1000 genomes]
rs6097939	0.94[ASN][1000 genomes]
rs6097940	0.94[ASN][1000 genomes]
rs6097941	0.94[ASN][1000 genomes]
rs6097945	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097946	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097963	0.85[ASN][1000 genomes]
rs73624107	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73624108	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73624110	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793033	0.91[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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52983400-52986200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:52984600-52986000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:52984800-52986000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr20:52984800-52986000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr20:52985000-52985800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:52985200-52986000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:52985200-52986200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52985200-52986200	Enhancers	HUES48 Cell Line	embryonic stem cell

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