Variant report

Variant	rs6123425
Chromosome Location	chr20:53494733-53494734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:53488399..53491672-chr20:53492910..53495826,3	MCF-7	breast:
2	chr20:53494550..53496057-chr3:64672192..64674727,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163638	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11696214	0.85[ASN][1000 genomes]
rs12625335	0.92[ASN][1000 genomes]
rs13038124	0.83[ASN][1000 genomes]
rs1398111	0.85[ASN][1000 genomes]
rs1398118	0.83[ASN][1000 genomes]
rs17000338	0.85[ASN][1000 genomes]
rs2203127	0.80[ASN][1000 genomes]
rs2870371	0.84[ASN][1000 genomes]
rs2870372	0.82[ASN][1000 genomes]
rs34354535	0.83[ASN][1000 genomes]
rs35146414	0.84[ASN][1000 genomes]
rs36033340	0.85[ASN][1000 genomes]
rs4809974	0.91[ASN][1000 genomes]
rs4809975	0.83[ASN][1000 genomes]
rs4811543	0.83[ASN][1000 genomes]
rs4811545	0.91[ASN][1000 genomes]
rs4811548	0.93[ASN][1000 genomes]
rs6023670	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023671	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023672	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60432774	0.82[ASN][1000 genomes]
rs6064124	0.82[ASN][1000 genomes]
rs6064126	0.87[ASN][1000 genomes]
rs6064127	0.82[ASN][1000 genomes]
rs6064130	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6064132	0.83[ASN][1000 genomes]
rs6064133	0.81[ASN][1000 genomes]
rs6064134	0.81[ASN][1000 genomes]
rs6064135	0.91[ASN][1000 genomes]
rs6064137	0.93[ASN][1000 genomes]
rs6069019	0.89[ASN][1000 genomes]
rs6069023	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6069026	0.85[ASN][1000 genomes]
rs6069030	0.85[ASN][1000 genomes]
rs6069031	0.85[ASN][1000 genomes]
rs6069034	0.83[ASN][1000 genomes]
rs6069036	0.88[ASN][1000 genomes]
rs6069038	0.91[ASN][1000 genomes]
rs6069043	0.93[ASN][1000 genomes]
rs6123427	0.91[ASN][1000 genomes]
rs6127305	0.89[ASN][1000 genomes]
rs6127308	0.93[ASN][1000 genomes]
rs6127311	0.93[ASN][1000 genomes]
rs6127315	0.91[ASN][1000 genomes]
rs6127316	0.88[ASN][1000 genomes]
rs6127317	0.91[ASN][1000 genomes]
rs6127318	0.91[ASN][1000 genomes]
rs7263291	0.81[ASN][1000 genomes]
rs73624159	0.89[ASN][1000 genomes]
rs8119241	0.80[ASN][1000 genomes]
rs958026	0.85[ASN][1000 genomes]
rs958880	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs992981	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	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:0 , 50 per page) page:

No data

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

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