Variant report

Variant	rs1542523
Chromosome Location	chr20:52910302-52910303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52908727..52910556-chr20:52917946..52923275,4	MCF-7	breast:
2	chr20:52862270..52864864-chr20:52907686..52911430,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1293132	0.89[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1293137	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1293144	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1298513	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1343080	0.80[EUR][1000 genomes]
rs1382010	0.81[EUR][1000 genomes]
rs1418924	0.81[EUR][1000 genomes]
rs1542522	0.84[EUR][1000 genomes]
rs2153964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2185849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616330	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2616335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870320	0.83[EUR][1000 genomes]
rs292120	0.81[EUR][1000 genomes]
rs292123	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs292125	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs292126	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs292132	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs292139	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs292141	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs292143	0.85[EUR][1000 genomes]
rs292144	0.86[EUR][1000 genomes]
rs292146	0.84[EUR][1000 genomes]
rs6013944	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6013960	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6023082	0.84[EUR][1000 genomes]
rs6097895	0.82[EUR][1000 genomes]
rs6097896	0.82[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52909400-52910400	Enhancers	Fetal Lung	lung
2	chr20:52909600-52910400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr20:52909800-52910400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:52909800-52910600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:52910000-52910400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52910000-52910400	Weak transcription	Hela-S3	cervix
7	chr20:52910000-52915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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