Variant report

Variant	rs6106949
Chromosome Location	chr20:24776446-24776447
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	chr20:24770878..24773860-chr20:24773955..24776847,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1109682	0.95[AFR][1000 genomes]
rs56888172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57470115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57844623	0.89[AMR][1000 genomes]
rs57923170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58679653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59254947	0.92[AFR][1000 genomes]
rs60419449	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6114859	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6114863	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6114867	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6114869	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6114871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6114872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6114874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61190938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7260865	0.89[AMR][1000 genomes]
rs73331358	0.89[AMR][1000 genomes]
rs73333459	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73333468	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73333473	0.83[AFR][1000 genomes]
rs73333486	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73333500	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73335424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7360504	0.86[AFR][1000 genomes]
rs8116690	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs8123123	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8123361	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs911173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1059270	chr20:24741923-24787243	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24774000-24777000	Weak transcription	Spleen	Spleen
2	chr20:24774000-24783000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:24775800-24776800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:24775800-24777200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:24775800-24778000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr20:24776000-24776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:24776200-24776600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:24776200-24776600	Enhancers	HSMM	muscle
9	chr20:24776400-24776600	Enhancers	Fetal Lung	lung
10	chr20:24776400-24776600	Enhancers	HSMMtube	muscle
11	chr20:24776400-24777400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:24776400-24779000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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