Variant report

Variant	rs283279
Chromosome Location	chr20:53537156-53537157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53281502..53283997-chr20:53536510..53538285,2	MCF-7	breast:
2	chr20:53528274..53530269-chr20:53537071..53540114,3	MCF-7	breast:
3	chr20:53533974..53538629-chr20:53538672..53542933,6	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1398113	0.87[EUR][1000 genomes]
rs17267366	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2022186	0.87[EUR][1000 genomes]
rs2048504	0.85[CEU][hapmap]
rs283277	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283278	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283280	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs365610	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs366808	0.94[CEU][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs431022	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs444445	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4811542	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4811544	0.86[EUR][1000 genomes]
rs4811547	0.85[TSI][hapmap]
rs6014211	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6023645	0.89[CEU][hapmap]
rs6023649	0.82[TSI][hapmap]
rs6023655	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6023669	0.87[EUR][1000 genomes]
rs6023673	0.87[EUR][1000 genomes]
rs6064129	0.88[EUR][1000 genomes]
rs6069016	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6123426	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6123433	0.86[EUR][1000 genomes]
rs6127310	0.85[EUR][1000 genomes]
rs6127331	0.87[EUR][1000 genomes]
rs6127333	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6127334	0.87[EUR][1000 genomes]
rs7263291	0.83[TSI][hapmap]
rs912507	0.94[CEU][hapmap]
rs912510	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs912511	0.87[EUR][1000 genomes]
rs912512	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3376519	chr20:53513594-53542087	Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs283279	ATP9A	cis	cerebellum	SCAN
rs283279	PFDN4	cis	cerebellum	SCAN
rs283279	FAM65C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53536600-53537600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links