Variant report

Variant	rs56122279
Chromosome Location	chr2:11853585-11853586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11850883..11854568-chr2:11860179..11862646,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs56037558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56266446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56958924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57097271	0.98[AFR][1000 genomes]
rs57245099	0.86[AFR][1000 genomes]
rs58429439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59002621	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61153226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61602903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73915489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73915494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73915497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73915498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73915500	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11844200-11854200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:11844600-11856400	Weak transcription	Psoas Muscle	Psoas
3	chr2:11848800-11854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:11848800-11855400	Weak transcription	Pancreas	Pancrea
5	chr2:11849000-11854400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:11850600-11856400	Weak transcription	Hela-S3	cervix
7	chr2:11850800-11856200	Weak transcription	Right Atrium	heart
8	chr2:11851400-11856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:11851400-11856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:11851600-11855600	Weak transcription	Liver	Liver
11	chr2:11851800-11856600	Weak transcription	Fetal Lung	lung
12	chr2:11851800-11856800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:11852000-11859200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:11852200-11858600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:11852400-11858800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:11852600-11853600	Enhancers	NHEK	skin
17	chr2:11852600-11856000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:11852600-11856200	Weak transcription	Ovary	ovary
19	chr2:11852600-11859400	Weak transcription	Brain Substantia Nigra	brain
20	chr2:11852600-11860600	Weak transcription	Esophagus	oesophagus
21	chr2:11852800-11858800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:11852800-11859200	Weak transcription	Brain Angular Gyrus	brain
23	chr2:11853000-11856600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:11853000-11856600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:11853000-11856800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:11853200-11855400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:11853200-11856200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:11853200-11856200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:11853400-11856800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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