Variant report

Variant	rs28854225
Chromosome Location	chr4:87801333-87801334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87514088..87517377-chr4:87799089..87802650,3	MCF-7	breast:
2	chr4:87799011..87801836-chr4:87812116..87814217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109339	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029698	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10034541	0.92[EUR][1000 genomes]
rs1075989	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12186239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13103212	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13112444	0.80[EUR][1000 genomes]
rs13114907	0.87[EUR][1000 genomes]
rs13117826	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13131035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13131194	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13134746	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13143520	0.90[EUR][1000 genomes]
rs13147739	0.86[EUR][1000 genomes]
rs13147942	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13151671	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13151797	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13434404	0.92[EUR][1000 genomes]
rs2705623	0.96[EUR][1000 genomes]
rs28407685	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28439108	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28447475	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28457189	0.92[EUR][1000 genomes]
rs28458234	0.92[EUR][1000 genomes]
rs28502831	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594717	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28610346	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28620528	0.90[EUR][1000 genomes]
rs28629974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661703	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28664715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28706796	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28729679	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28886889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34991149	0.92[EUR][1000 genomes]
rs35480728	0.90[EUR][1000 genomes]
rs35667731	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36053558	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4693788	0.85[EUR][1000 genomes]
rs71605624	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71605686	0.96[EUR][1000 genomes]
rs71605687	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71605688	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71605691	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71605693	0.90[EUR][1000 genomes]
rs7683045	0.96[EUR][1000 genomes]
rs9993812	0.92[EUR][1000 genomes]
rs9999001	0.88[EUR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 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	chr4:87800600-87801600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:87801000-87801600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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