Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59145235..59147657-chr12:59160178..59163075,2	MCF-7	breast:

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

rs_ID	r²[population]
rs1121270	0.82[AFR][1000 genomes]
rs1353610	0.97[EUR][1000 genomes]
rs1353611	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1391021	0.84[AFR][1000 genomes]
rs1497235	0.82[AFR][1000 genomes]
rs1531138	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124516	0.84[AFR][1000 genomes]
rs2605422	1.00[EUR][1000 genomes]
rs2605426	0.84[AFR][1000 genomes]
rs2645865	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645867	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712504	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712505	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712508	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2712510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712511	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712513	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712514	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712515	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712516	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712517	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1049807	chr12:59069437-59227711	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv826390	chr12:59097995-59199786	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2712503	CDK4	cis	cerebellum	SCAN
rs2712503	GTSF1	cis	cerebellum	SCAN
rs2712503	TARBP2	cis	parietal	SCAN
rs2712503	SMUG1	cis	cerebellum	SCAN
rs2712503	ZNF385A	cis	parietal	SCAN
rs2712503	SMUG1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59140000-59150600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:59143600-59145600	Enhancers	NHDF-Ad	bronchial
3	chr12:59143600-59146400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:59143800-59145800	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr12:59144800-59145800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:59144800-59146800	Enhancers	NHLF	lung
7	chr12:59144800-59151200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:59145200-59150600	Weak transcription	NH-A	brain
9	chr12:59145400-59145600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:59145400-59146200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:59145400-59150800	Weak transcription	Muscle Satellite Cultured Cells	--

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