Variant report

Variant	rs6123426
Chromosome Location	chr20:53494866-53494867
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	chr20:53488399..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: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1398113	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1398117	0.83[EUR][1000 genomes]
rs1512061	0.87[EUR][1000 genomes]
rs1512065	0.82[EUR][1000 genomes]
rs17267366	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2048504	0.84[EUR][1000 genomes]
rs283277	0.88[EUR][1000 genomes]
rs283278	0.85[EUR][1000 genomes]
rs283279	0.85[EUR][1000 genomes]
rs283280	0.84[EUR][1000 genomes]
rs365610	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs366808	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs431022	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs444445	0.84[EUR][1000 genomes]
rs4811538	0.83[EUR][1000 genomes]
rs4811542	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811544	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4811546	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4811547	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6014185	0.85[EUR][1000 genomes]
rs6014211	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6023625	0.80[EUR][1000 genomes]
rs6023645	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6023655	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023669	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023673	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6064129	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6069016	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6069037	0.83[EUR][1000 genomes]
rs6069039	0.83[EUR][1000 genomes]
rs6127309	0.81[EUR][1000 genomes]
rs6127310	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912507	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs912510	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912511	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912512	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

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