Variant report

Variant	rs12492415
Chromosome Location	chr3:20693731-20693732
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	chr3:20691277..20693337-chr3:20693426..20695477,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12489862	0.90[EUR][1000 genomes]
rs12496154	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1500414	0.94[EUR][1000 genomes]
rs1827229	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2036599	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4857965	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4857966	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4858246	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858247	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62242114	0.91[EUR][1000 genomes]
rs6768859	0.85[EUR][1000 genomes]
rs6775875	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6778472	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6780133	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6787288	0.90[EUR][1000 genomes]
rs7611714	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs904826	0.90[EUR][1000 genomes]
rs9833959	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835418	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9856793	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861687	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9876444	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883871	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv876598	chr3:20242143-20970042	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv876599	chr3:20264950-20813009	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv876603	chr3:20626326-20727885	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv460460	chr3:20638228-20718124	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	nsv589866	chr3:20638228-20718124	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
8	nsv876604	chr3:20646486-20710994	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv460462	chr3:20684823-20708251	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv589867	chr3:20684823-20708251	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20688000-20693800	Enhancers	NHDF-Ad	bronchial
2	chr3:20690600-20693800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:20690800-20693800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:20690800-20693800	Weak transcription	NHLF	lung
5	chr3:20692000-20693800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:20693000-20693800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:20693200-20693800	Enhancers	Brain Germinal Matrix	brain
8	chr3:20693200-20693800	Enhancers	Fetal Lung	lung
9	chr3:20693200-20693800	Enhancers	NH-A	brain
10	chr3:20693200-20694000	Enhancers	Fetal Brain Female	brain
11	chr3:20693200-20694200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:20693400-20694600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:20693600-20694000	Enhancers	Fetal Muscle Leg	muscle

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