Variant report

Variant	rs6023655
Chromosome Location	chr20:53479658-53479659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:53479565-53479942	H1-neurons	neurons:	n/a	n/a
2	GATA3	chr20:53479315-53479673	SH-SY5Y	brain:	n/a	chr20:53479635-53479656
3	POLR2A	chr20:53479552-53480037	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:53471731..53474683-chr20:53478137..53479818,2	K562	blood:
2	chr20:53476260..53477988-chr20:53478518..53480818,2	MCF-7	breast:
3	chr20:53479571..53482526-chr20:53495392..53497339,2	MCF-7	breast:
4	chr20:53471099..53474032-chr20:53476723..53479996,4	MCF-7	breast:
5	chr20:53478917..53482886-chr20:53482931..53485489,4	MCF-7	breast:
6	chr20:53479221..53481669-chr20:53481734..53483343,2	MCF-7	breast:

Variant related genes	Relation type
RNU4ATAC7P	TF binding region
ENSG00000252089	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1398113	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398117	0.82[EUR][1000 genomes]
rs1512061	0.86[EUR][1000 genomes]
rs1512065	0.84[EUR][1000 genomes]
rs17267366	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2048504	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs283277	0.85[EUR][1000 genomes]
rs283278	0.82[EUR][1000 genomes]
rs283279	0.83[EUR][1000 genomes]
rs283280	0.81[EUR][1000 genomes]
rs365610	0.83[EUR][1000 genomes]
rs366808	0.94[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs431022	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs444445	0.81[EUR][1000 genomes]
rs4811538	0.85[EUR][1000 genomes]
rs4811542	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4811544	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4811546	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs4811547	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6014185	0.86[EUR][1000 genomes]
rs6014211	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023624	0.81[EUR][1000 genomes]
rs6023625	0.82[EUR][1000 genomes]
rs6023645	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023669	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023673	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6064129	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6069016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6069037	0.82[EUR][1000 genomes]
rs6069039	0.82[EUR][1000 genomes]
rs6123426	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127310	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912507	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs912510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912511	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6023655	ATP9A	cis	cerebellum	SCAN
rs6023655	PFDN4	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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