Variant report

Variant	rs6013989
Chromosome Location	chr20:52982785-52982786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:42839047..42839970-chr20:52982175..52983148,2	MCF-7	breast:
2	chr20:49347583..49351619-chr20:52982625..52987672,5	MCF-7	breast:
3	chr20:52982598..52985363-chr20:52985830..52988598,3	MCF-7	breast:
4	chr20:52981982..52984941-chr20:53255246..53257720,2	MCF-7	breast:
5	chr20:52977120..52978918-chr20:52982695..52985421,2	MCF-7	breast:
6	chr20:52982179..52987061-chr20:52989270..52993345,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223891	Chromatin interaction
ENSG00000132823	Chromatin interaction
ENSG00000124171	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1014808	0.82[ASN][1000 genomes]
rs1407043	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs16999559	0.88[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16999597	0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs1841860	0.90[ASN][1000 genomes]
rs1923118	0.85[ASN][1000 genomes]
rs2126676	0.89[ASN][1000 genomes]
rs28406117	0.98[ASN][1000 genomes]
rs28429972	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56881371	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59924072	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6013987	0.98[ASN][1000 genomes]
rs6013997	0.87[ASN][1000 genomes]
rs6013999	0.85[ASN][1000 genomes]
rs6014003	0.85[ASN][1000 genomes]
rs6014004	0.84[ASN][1000 genomes]
rs6014005	0.85[ASN][1000 genomes]
rs6023153	0.94[ASN][1000 genomes]
rs6023154	0.94[ASN][1000 genomes]
rs6023155	0.95[ASN][1000 genomes]
rs6023156	0.95[ASN][1000 genomes]
rs6023158	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023163	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023164	0.99[ASN][1000 genomes]
rs6023178	0.84[ASN][1000 genomes]
rs6023179	0.84[ASN][1000 genomes]
rs6023180	0.88[ASN][1000 genomes]
rs6023181	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6023185	0.83[ASN][1000 genomes]
rs6023189	0.86[ASN][1000 genomes]
rs6023192	0.85[ASN][1000 genomes]
rs6023193	0.85[ASN][1000 genomes]
rs6023203	0.85[ASN][1000 genomes]
rs6091856	0.91[ASN][1000 genomes]
rs6097934	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6097938	0.90[ASN][1000 genomes]
rs6097939	0.93[ASN][1000 genomes]
rs6097940	0.93[ASN][1000 genomes]
rs6097941	0.93[ASN][1000 genomes]
rs6097945	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6097946	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6097963	0.85[ASN][1000 genomes]
rs73624107	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73624108	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73624110	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs793033	0.90[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	nsv527610	chr20:52980099-52984431	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52976600-52983400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:52976600-52985200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr20:52977600-52985200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr20:52977800-52985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:52979200-52984800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr20:52979800-52984600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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