Variant report

Variant	rs56299926
Chromosome Location	chr20:24855925-24855926
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: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1029032	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11087480	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11700139	1.00[ASN][1000 genomes]
rs11700161	1.00[ASN][1000 genomes]
rs11906401	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11906511	0.91[EUR][1000 genomes]
rs1571772	1.00[ASN][1000 genomes]
rs2150644	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651048	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55681373	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55905952	1.00[ASN][1000 genomes]
rs55979003	1.00[ASN][1000 genomes]
rs56000345	1.00[ASN][1000 genomes]
rs56053259	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56148678	0.91[EUR][1000 genomes]
rs56249107	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56406017	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58353086	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036939	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036940	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036948	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6049996	1.00[ASN][1000 genomes]
rs6050002	1.00[ASN][1000 genomes]
rs6050026	0.89[EUR][1000 genomes]
rs6050052	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6050056	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6050066	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6050121	0.88[AMR][1000 genomes]
rs6050123	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6050124	0.88[AMR][1000 genomes]
rs6076279	1.00[ASN][1000 genomes]
rs6076281	1.00[ASN][1000 genomes]
rs6076283	1.00[ASN][1000 genomes]
rs6076288	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076289	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076291	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076293	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083630	1.00[ASN][1000 genomes]
rs6083632	1.00[ASN][1000 genomes]
rs6083633	1.00[ASN][1000 genomes]
rs6083638	0.88[EUR][1000 genomes]
rs6083639	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083645	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083646	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083647	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083649	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6083650	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083651	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083653	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083657	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106957	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106965	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6106967	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114893	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62215819	1.00[ASN][1000 genomes]
rs62215821	1.00[ASN][1000 genomes]
rs62215822	1.00[ASN][1000 genomes]
rs62215823	1.00[ASN][1000 genomes]
rs62215824	1.00[ASN][1000 genomes]
rs62215826	1.00[ASN][1000 genomes]
rs6515535	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515552	0.80[AMR][1000 genomes]
rs7262604	1.00[ASN][1000 genomes]
rs7269852	1.00[ASN][1000 genomes]
rs73101427	1.00[ASN][1000 genomes]
rs73108128	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110258	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110260	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337207	1.00[ASN][1000 genomes]
rs7509561	1.00[ASN][1000 genomes]
rs8114708	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114760	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117102	1.00[ASN][1000 genomes]
rs8117164	1.00[ASN][1000 genomes]
rs8119191	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120506	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123541	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914308	0.89[EUR][1000 genomes]
rs914309	0.87[AMR][1000 genomes];0.82[EUR][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:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24853200-24863400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24855800-24856000	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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