Variant report

Variant	rs2575780
Chromosome Location	chr3:87046959-87046960
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	chr3:87039512..87041163-chr3:87044604..87047254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206538	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12152340	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1370040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370042	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1436647	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821750	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898274	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2118078	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2262594	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2262595	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2575775	0.80[EUR][1000 genomes]
rs2575782	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2575783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575784	0.85[EUR][1000 genomes]
rs2575794	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2575799	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2575800	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2660767	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2660769	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2660772	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2660773	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2660774	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2660779	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2660796	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660797	0.83[EUR][1000 genomes]
rs2660798	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62259566	0.84[AFR][1000 genomes]
rs990159	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87046200-87048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:87046200-87048200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:87046400-87047600	Weak transcription	NHDF-Ad	bronchial
4	chr3:87046400-87051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:87046600-87047200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:87046600-87047600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:87046600-87047600	Weak transcription	HSMM	muscle
8	chr3:87046600-87051200	Weak transcription	Placenta	Placenta
9	chr3:87046800-87048800	Weak transcription	Placenta Amnion	Placenta Amnion

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