Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143691583..143692190-chr3:144216201..144216835,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1178898	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1178902	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13076501	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527231	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1656986	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1725559	1.00[CHB][hapmap]
rs1726523	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1726525	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1726537	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1880902	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2575182	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2575187	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2694958	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2717378	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4511940	1.00[ASN][1000 genomes]
rs4681332	0.93[EUR][1000 genomes]
rs759968	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931773	1.00[CHB][hapmap]
rs9845422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852425	1.00[ASN][1000 genomes]
rs9864125	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871303	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1011685	chr3:143959237-144218424	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536751	chr3:143959237-144218424	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2756108	chr3:144177836-144301659	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877571	chr3:144188561-144291254	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9857731	CHAF1A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144215400-144216600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:144215400-144217400	Weak transcription	HUVEC	blood vessel
3	chr3:144215600-144220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:144216200-144216400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:144216200-144216600	Enhancers	H1 Cell Line	embryonic stem cell

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