Variant report

Variant	rs6083652
Chromosome Location	chr20:24854343-24854344
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	chr20:24811551..24814210-chr20:24854321..24856444,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1029031	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1029033	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1113872	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1122607	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11697463	0.82[EUR][1000 genomes]
rs11700139	0.82[EUR][1000 genomes]
rs11700161	0.82[EUR][1000 genomes]
rs11905160	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151907	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1331285	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1331290	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1411892	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1411894	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1411895	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1413069	0.84[EUR][1000 genomes]
rs1831483	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1888655	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064404	1.00[CHB][hapmap]
rs4239751	1.00[CHB][hapmap]
rs4815358	1.00[CHB][hapmap]
rs4815359	1.00[CHB][hapmap]
rs55702326	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55905952	0.85[EUR][1000 genomes]
rs55979003	0.85[EUR][1000 genomes]
rs56000345	0.80[EUR][1000 genomes]
rs56106395	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56179484	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036915	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036943	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036946	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036951	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036955	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036967	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6036968	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6036970	0.86[EUR][1000 genomes]
rs6036971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036972	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049996	0.85[EUR][1000 genomes]
rs6050000	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6050002	0.84[EUR][1000 genomes]
rs6050007	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050051	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6050058	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6050070	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6050073	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6050074	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6050114	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050115	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050116	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050117	0.92[EUR][1000 genomes]
rs6050119	0.92[EUR][1000 genomes]
rs6050120	0.91[EUR][1000 genomes]
rs6050122	0.87[EUR][1000 genomes]
rs6050125	0.82[EUR][1000 genomes]
rs6076279	0.83[EUR][1000 genomes]
rs6076281	0.84[EUR][1000 genomes]
rs6076283	0.84[EUR][1000 genomes]
rs6076290	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6076292	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6076299	0.80[EUR][1000 genomes]
rs6083628	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6083630	0.83[EUR][1000 genomes]
rs6083631	0.84[EUR][1000 genomes]
rs6083632	0.84[EUR][1000 genomes]
rs6083633	0.84[EUR][1000 genomes]
rs6083656	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6083658	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6083672	0.91[AMR][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6083714	1.00[CHB][hapmap]
rs6106968	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6106969	0.90[EUR][1000 genomes]
rs6114915	0.84[EUR][1000 genomes]
rs6114918	0.84[EUR][1000 genomes]
rs6114921	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138396	0.89[AFR][1000 genomes]
rs62215819	0.80[EUR][1000 genomes]
rs62215823	0.83[EUR][1000 genomes]
rs62215824	0.84[EUR][1000 genomes]
rs62215826	0.84[EUR][1000 genomes]
rs62215832	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6515538	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7262604	0.85[EUR][1000 genomes]
rs73101427	0.80[EUR][1000 genomes]
rs7509561	0.82[EUR][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs765834	1.00[CHB][hapmap]
rs8117102	0.85[EUR][1000 genomes]
rs8117164	0.85[EUR][1000 genomes]
rs914310	0.89[EUR][1000 genomes]
rs914311	0.87[EUR][1000 genomes]
rs944503	0.80[AMR][1000 genomes]
rs961218	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24852800-24854600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr20:24853000-24854400	Enhancers	Primary B cells from cord blood	blood
3	chr20:24853000-24854400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:24853000-24854400	Enhancers	Dnd41	blood
5	chr20:24853000-24854600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr20:24853200-24854400	Enhancers	Primary hematopoietic stem cells	blood
7	chr20:24853200-24863400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:24853600-24854400	Enhancers	Primary B cells from peripheral blood	blood
9	chr20:24853600-24855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:24854200-24855200	Weak transcription	Spleen	Spleen

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