Variant report

Variant	rs1398113
Chromosome Location	chr20:53488219-53488220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53487853..53490611-chr20:53501403..53504058,2	MCF-7	breast:
2	chr20:53486873..53489531-chr20:53490291..53491928,2	MCF-7	breast:
3	chr20:42836318..42837241-chr20:53487584..53488313,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DOK5-2	chr20:53488074-53488248	NONHSAT080422

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1398117	0.84[EUR][1000 genomes]
rs1512061	0.88[EUR][1000 genomes]
rs1512065	0.81[EUR][1000 genomes]
rs17267366	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2048504	0.83[EUR][1000 genomes]
rs283277	0.87[EUR][1000 genomes]
rs283278	0.86[EUR][1000 genomes]
rs283279	0.87[EUR][1000 genomes]
rs283280	0.85[EUR][1000 genomes]
rs365610	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs366808	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs431022	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs444445	0.83[EUR][1000 genomes]
rs4811538	0.82[EUR][1000 genomes]
rs4811542	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4811544	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4811546	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs4811547	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6014185	0.83[EUR][1000 genomes]
rs6014211	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6023645	0.84[CEU][hapmap]
rs6023655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6023669	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6023673	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6064129	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6069016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6069033	0.80[EUR][1000 genomes]
rs6069037	0.84[EUR][1000 genomes]
rs6069039	0.84[EUR][1000 genomes]
rs6123426	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6127309	0.83[EUR][1000 genomes]
rs6127310	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs912507	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs912510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs912511	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs912512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3396113	chr20:53486545-53490143	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No data

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