Variant report

Variant	rs2022186
Chromosome Location	chr20:53568212-53568213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1125961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499870	1.00[ASN][1000 genomes]
rs17267366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283277	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs283278	0.86[EUR][1000 genomes]
rs283279	0.87[EUR][1000 genomes]
rs283280	0.85[EUR][1000 genomes]
rs288829	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs365610	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs366808	0.89[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs373968	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs392646	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs415667	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs423867	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs430767	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs431022	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs444445	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs451817	0.86[ASN][1000 genomes]
rs4811542	0.81[EUR][1000 genomes]
rs4811547	0.85[TSI][hapmap]
rs6014211	0.81[EUR][1000 genomes]
rs6023645	0.84[CEU][hapmap]
rs6023655	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs6069016	0.94[CEU][hapmap]
rs6123426	0.94[CEU][hapmap]
rs6123433	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127331	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127333	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127345	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71196476	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs912507	0.89[CEU][hapmap]
rs912510	0.94[CEU][hapmap]
rs912512	0.94[CEU][hapmap]

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
rs2022186	PFDN4	cis	cerebellum	SCAN
rs2022186	ATP9A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53558400-53569600	Weak transcription	Fetal Brain Male	brain

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