Variant report

Variant	rs6097590
Chromosome Location	chr20:52430071-52430072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:125398553..125400192-chr20:52427859..52430719,2	MCF-7	breast:
2	chr17:57920235..57924333-chr20:52429102..52433738,4	MCF-7	breast:
3	chr20:52429323..52432277-chr9:134928872..134931515,2	MCF-7	breast:
4	chr12:47501255..47503970-chr20:52428437..52430866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150991	Chromatin interaction
ENSG00000265345	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10211708	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10211779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11904880	0.83[AFR][1000 genomes]
rs16998448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097595	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097599	0.82[AFR][1000 genomes]
rs6097600	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097601	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67891850	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7273809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272038	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272049	1.00[AFR][1000 genomes]
rs8120680	0.89[EUR][1000 genomes]
rs8126424	1.00[AFR][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52422600-52431400	Weak transcription	HepG2	liver
2	chr20:52423600-52432400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr20:52423800-52430400	Weak transcription	NHDF-Ad	bronchial
4	chr20:52423800-52436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:52426200-52430400	Weak transcription	NHEK	skin
6	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:52426400-52431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:52426400-52436000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:52427200-52434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr20:52427800-52430200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr20:52429800-52430600	Enhancers	Fetal Stomach	stomach
12	chr20:52429800-52432000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52430000-52430200	Enhancers	Esophagus	oesophagus
14	chr20:52430000-52430600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:52430000-52430600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:52430000-52431600	Enhancers	A549	lung
17	chr20:52430000-52432000	Enhancers	Fetal Lung	lung

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