Variant report

Variant	rs6064129
Chromosome Location	chr20:53497624-53497625
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:53485625..53487827-chr20:53496627..53498549,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1398113	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1398117	0.86[EUR][1000 genomes]
rs1512061	0.87[EUR][1000 genomes]
rs17267366	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2048504	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs283277	0.88[EUR][1000 genomes]
rs283278	0.88[EUR][1000 genomes]
rs283279	0.88[EUR][1000 genomes]
rs283280	0.87[EUR][1000 genomes]
rs365610	0.86[EUR][1000 genomes]
rs366808	0.94[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs431022	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs444445	0.84[EUR][1000 genomes]
rs4811538	0.81[EUR][1000 genomes]
rs4811542	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811544	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4811546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4811547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs6014185	0.82[EUR][1000 genomes]
rs6014211	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6023645	0.89[CEU][hapmap]
rs6023655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023669	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023673	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6069016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6069033	0.82[EUR][1000 genomes]
rs6069037	0.86[EUR][1000 genomes]
rs6069039	0.86[EUR][1000 genomes]
rs6123426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127309	0.81[EUR][1000 genomes]
rs6127310	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127333	0.80[EUR][1000 genomes]
rs912507	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs912510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912511	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv521883	chr20:53497139-53563837	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv524442	chr20:53497139-53563837	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6064129	PFDN4	cis	cerebellum	SCAN
rs6064129	ATP9A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53495400-53508800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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