Variant report

Variant	rs6023474
Chromosome Location	chr20:53284144-53284145
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:53283290..53284914-chr3:64513834..64516578,2	MCF-7	breast:
2	chr20:53282910..53285557-chr7:133594422..133596091,2	MCF-7	breast:
3	chr20:53283455..53285734-chr3:64506182..64507970,2	MCF-7	breast:
4	chr20:53263266..53270310-chr20:53278109..53284478,8	MCF-7	breast:
5	chr20:53283718..53285867-chr3:64515756..64517189,9	MCF-7	breast:
6	chr20:53281054..53285156-chr3:64517678..64520991,4	MCF-7	breast:
7	chr20:53283717..53285430-chr3:64475712..64477407,2	MCF-7	breast:
8	chr20:53272079..53274152-chr20:53283538..53285655,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163638	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1012643	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13040265	1.00[CHD][hapmap]
rs1474763	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1569985	1.00[CHD][hapmap]
rs1983702	1.00[CHD][hapmap]
rs1997834	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs2870333	1.00[CHD][hapmap]
rs2870337	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2870340	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2904389	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4334548	1.00[CHD][hapmap]
rs4362623	0.85[EUR][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6014111	0.83[EUR][1000 genomes]
rs6014112	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023367	1.00[CHD][hapmap]
rs6023406	1.00[CHD][hapmap]
rs6023423	1.00[CHD][hapmap]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap]
rs6023475	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023477	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6064093	1.00[CHD][hapmap]
rs6064102	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6068924	1.00[CHD][hapmap]
rs6068935	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6098108	1.00[CHD][hapmap]
rs6098158	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs6123404	1.00[CHD][hapmap];0.94[GIH][hapmap]
rs6127251	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7263678	1.00[CHD][hapmap]
rs7270451	1.00[CHD][hapmap]
rs7270971	1.00[CHD][hapmap]
rs8115071	1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][hapmap]

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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53280600-53285000	Weak transcription	Ovary	ovary
2	chr20:53280800-53285000	Weak transcription	Fetal Heart	heart
3	chr20:53281800-53285600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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