Variant report

Variant	rs1109682
Chromosome Location	chr20:24771214-24771215
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	chr20:24770878..24773860-chr20:24773955..24776847,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11908480	1.00[EUR][1000 genomes]
rs1467769	0.84[EUR][1000 genomes]
rs2151460	0.82[EUR][1000 genomes]
rs34799975	0.82[EUR][1000 genomes]
rs56888172	0.95[AFR][1000 genomes]
rs57470115	0.95[AFR][1000 genomes]
rs57923170	0.95[AFR][1000 genomes]
rs58679653	0.95[AFR][1000 genomes]
rs59254947	0.88[AFR][1000 genomes]
rs6036921	0.84[EUR][1000 genomes]
rs6036927	0.84[EUR][1000 genomes]
rs6036932	0.82[EUR][1000 genomes]
rs6036938	0.82[EUR][1000 genomes]
rs6036944	0.82[EUR][1000 genomes]
rs60419449	0.88[AFR][1000 genomes]
rs6050001	0.84[EUR][1000 genomes]
rs6050003	0.84[EUR][1000 genomes]
rs6050005	0.84[EUR][1000 genomes]
rs6050006	0.84[EUR][1000 genomes]
rs6050013	0.84[EUR][1000 genomes]
rs6050014	0.84[EUR][1000 genomes]
rs6050016	0.92[EUR][1000 genomes]
rs6050017	0.84[EUR][1000 genomes]
rs6050019	0.84[EUR][1000 genomes]
rs6050023	0.84[EUR][1000 genomes]
rs6050041	0.82[EUR][1000 genomes]
rs6050042	0.82[EUR][1000 genomes]
rs6050045	0.82[EUR][1000 genomes]
rs6050047	0.82[EUR][1000 genomes]
rs6050049	0.82[EUR][1000 genomes]
rs6106949	0.95[AFR][1000 genomes]
rs6106952	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6114857	0.86[AMR][1000 genomes]
rs6114859	0.81[AFR][1000 genomes]
rs6114863	0.88[AFR][1000 genomes]
rs6114867	0.92[AFR][1000 genomes]
rs6114869	0.94[AFR][1000 genomes]
rs6114871	0.92[AFR][1000 genomes]
rs6114872	0.95[AFR][1000 genomes]
rs6114874	0.95[AFR][1000 genomes]
rs6114875	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6114886	0.84[EUR][1000 genomes]
rs6114888	0.84[EUR][1000 genomes]
rs61190938	0.95[AFR][1000 genomes]
rs7262621	1.00[EUR][1000 genomes]
rs7262640	1.00[EUR][1000 genomes]
rs73331396	0.86[AMR][1000 genomes]
rs73331399	0.86[AMR][1000 genomes]
rs73333403	0.86[AMR][1000 genomes]
rs73333424	0.86[AMR][1000 genomes]
rs73333459	0.86[AFR][1000 genomes]
rs73333468	0.91[AFR][1000 genomes]
rs73333473	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73333486	0.92[AFR][1000 genomes]
rs73333500	0.91[AFR][1000 genomes]
rs73335424	0.95[AFR][1000 genomes]
rs73335427	0.95[AFR][1000 genomes]
rs73335453	0.95[AFR][1000 genomes]
rs73335473	0.84[EUR][1000 genomes]
rs73335492	0.84[EUR][1000 genomes]
rs73337274	0.84[EUR][1000 genomes]
rs73339206	0.92[EUR][1000 genomes]
rs7360504	0.82[AFR][1000 genomes]
rs7360533	0.86[AMR][1000 genomes]
rs73903961	1.00[EUR][1000 genomes]
rs73903963	1.00[EUR][1000 genomes]
rs73903968	1.00[EUR][1000 genomes]
rs8116690	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs8119131	0.84[EUR][1000 genomes]
rs8120183	0.86[AMR][1000 genomes]
rs8123123	0.88[AFR][1000 genomes]
rs8123361	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs911173	0.95[AFR][1000 genomes]
rs914306	0.92[EUR][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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24767400-24772400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr20:24769800-24771400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:24770000-24771400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24770400-24771600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:24770600-24771800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:24771200-24771400	Enhancers	Fetal Muscle Leg	muscle

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