Variant report

Variant	rs2870289
Chromosome Location	chr20:52432787-52432788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57920235..57924333-chr20:52429102..52433738,4	MCF-7	breast:
2	chr20:45989026..45990634-chr20:52430847..52433559,2	MCF-7	breast:
3	chr2:160568775..160570535-chr20:52431319..52433278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136536	Chromatin interaction
ENSG00000226266	Chromatin interaction

Extended variants
information (count: 32 )
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]
rs6097589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097590	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:4 , 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	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52423800-52436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:52426400-52436000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:52427200-52434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr20:52430400-52432800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr20:52430600-52434200	Weak transcription	Fetal Stomach	stomach
7	chr20:52431200-52432800	Enhancers	Primary T cells from cord blood	blood
8	chr20:52431600-52436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52431600-52439400	Weak transcription	A549	lung
10	chr20:52431800-52432800	Enhancers	GM12878-XiMat	blood
11	chr20:52431800-52435800	Weak transcription	Thymus	Thymus
12	chr20:52431800-52436000	Weak transcription	HepG2	liver
13	chr20:52432000-52433400	Weak transcription	Fetal Lung	lung

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