Variant report

Variant	rs2063520
Chromosome Location	chr20:53459611-53459612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53419453..53421420-chr20:53458481..53461385,2	MCF-7	breast:
2	chr20:53455825..53458211-chr20:53458861..53461984,3	MCF-7	breast:
3	chr20:53458659..53460997-chr21:40686277..40688957,2	MCF-7	breast:
4	chr20:53456314..53458987-chr20:53459309..53462293,2	MCF-7	breast:
5	chr20:53458657..53461544-chr20:53468848..53472413,4	MCF-7	breast:
6	chr20:53458903..53460576-chr20:53530268..53532313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10854195	0.83[JPT][hapmap]
rs1355565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512057	0.82[JPT][hapmap]
rs1512058	0.83[JPT][hapmap]
rs1512059	0.86[EUR][1000 genomes]
rs1543077	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025129	0.84[YRI][hapmap]
rs2063518	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2063521	0.81[AFR][1000 genomes]
rs2870370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331572	0.83[JPT][hapmap]
rs6014183	0.82[JPT][hapmap]
rs6023636	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6023640	0.90[YRI][hapmap]
rs6023646	0.82[JPT][hapmap]
rs6064116	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6064118	0.87[JPT][hapmap]
rs6064119	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6064120	0.83[JPT][hapmap]
rs6064121	0.83[JPT][hapmap]
rs6064123	0.83[JPT][hapmap]
rs6069006	0.83[JPT][hapmap]
rs6069012	0.83[JPT][hapmap]
rs6069013	0.85[JPT][hapmap]
rs6091986	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6098293	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127302	0.88[JPT][hapmap]
rs67320717	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925463	0.85[EUR][1000 genomes]
rs927653	0.82[AMR][1000 genomes];0.86[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53459600-53460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links