Variant report

Variant	rs6023180
Chromosome Location	chr20:53000158-53000159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52970500..52972765-chr20:52999038..53000852,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1007393	0.82[ASN][1000 genomes]
rs1014808	0.87[ASN][1000 genomes]
rs1321464	0.85[JPT][hapmap]
rs1321465	0.85[JPT][hapmap]
rs1321468	0.85[JPT][hapmap]
rs1358806	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1358807	0.89[ASN][1000 genomes]
rs1407043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590206	0.88[ASN][1000 genomes]
rs16999597	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1841860	0.81[ASN][1000 genomes]
rs1923118	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126676	0.82[ASN][1000 genomes]
rs28406117	0.87[ASN][1000 genomes]
rs28429972	0.89[ASN][1000 genomes]
rs2870329	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56881371	0.91[ASN][1000 genomes]
rs59924072	0.89[ASN][1000 genomes]
rs6013987	0.87[ASN][1000 genomes]
rs6013989	0.88[ASN][1000 genomes]
rs6013997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6013999	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6014003	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6014004	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6014005	0.83[CEU][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6014011	0.90[JPT][hapmap]
rs6023153	0.91[ASN][1000 genomes]
rs6023154	0.91[ASN][1000 genomes]
rs6023155	0.92[ASN][1000 genomes]
rs6023156	0.92[ASN][1000 genomes]
rs6023158	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6023163	0.89[ASN][1000 genomes]
rs6023164	0.89[ASN][1000 genomes]
rs6023178	0.88[ASN][1000 genomes]
rs6023179	0.88[ASN][1000 genomes]
rs6023181	0.80[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6023183	0.90[ASN][1000 genomes]
rs6023185	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023189	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6023192	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6023193	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6023197	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6023203	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6023227	0.85[JPT][hapmap]
rs6091856	0.81[ASN][1000 genomes]
rs6097934	0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6097938	0.87[ASN][1000 genomes]
rs6097939	0.92[ASN][1000 genomes]
rs6097940	0.91[ASN][1000 genomes]
rs6097941	0.91[ASN][1000 genomes]
rs6097944	0.83[CEU][hapmap]
rs6097945	0.86[ASN][1000 genomes]
rs6097946	0.86[ASN][1000 genomes]
rs6097955	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6097957	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6097963	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6097964	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6097967	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73624107	0.87[ASN][1000 genomes]
rs73624108	0.89[ASN][1000 genomes]
rs73624110	0.89[ASN][1000 genomes]
rs793033	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv962550	chr20:52999847-53001516	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52999400-53001200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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