Variant report

Variant	rs1293132
Chromosome Location	chr20:52903049-52903050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52823268..52824911-chr20:52902015..52904220,2	MCF-7	breast:
2	chr20:52902315..52904046-chr20:52922393..52924271,2	MCF-7	breast:
3	chr20:52897327..52899009-chr20:52901309..52903934,2	K562	blood:
4	chr20:52887148..52889148-chr20:52903005..52905781,2	MCF-7	breast:
5	chr20:52902572..52903442-chr20:52914717..52915419,2	MCF-7	breast:
6	chr20:52901774..52903726-chr20:52915299..52918140,2	MCF-7	breast:
7	chr20:52891487..52895363-chr20:52902222..52905146,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1293137	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1293144	0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1298513	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1382015	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1477730	0.82[ASN][1000 genomes]
rs1542523	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061721	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2153964	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2153965	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2185849	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2585418	0.81[CEU][hapmap]
rs2616330	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2616335	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs292120	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs292123	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs292125	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs292126	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs292132	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs292139	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs292141	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs292143	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs292144	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs292146	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs368933	0.87[CEU][hapmap]
rs6013925	0.81[CEU][hapmap]
rs6013944	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs6013960	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6023082	0.91[EUR][1000 genomes];0.83[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1293132	AURKA	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links