Variant report

Variant	rs58624586
Chromosome Location	chr3:53174676-53174677
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53173447..53176074-chr3:53189009..53191483,3	MCF-7	breast:
2	chr3:53172874..53174968-chr3:53193590..53195106,2	MCF-7	breast:
3	chr3:53171302..53172940-chr3:53173107..53174967,2	K562	blood:
4	chr3:53173740..53175835-chr3:53182321..53184485,2	MCF-7	breast:
5	chr3:53162607..53165548-chr3:53173123..53174790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3891626	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6785768	1.00[AMR][1000 genomes]
rs6787566	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798092	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965386	1.00[AMR][1000 genomes]
rs72965387	1.00[AMR][1000 genomes]
rs72965388	1.00[AMR][1000 genomes]
rs72965394	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965401	0.86[AFR][1000 genomes];1.00[AMR][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	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv3356898	chr3:53172512-53176810	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
3	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
6	chr3:53165800-53175400	Weak transcription	Placenta	Placenta
7	chr3:53169200-53176200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:53169200-53179000	Weak transcription	Fetal Lung	lung
9	chr3:53169200-53183800	Weak transcription	Right Ventricle	heart
10	chr3:53172200-53174800	Weak transcription	GM12878-XiMat	blood
11	chr3:53173000-53175200	Enhancers	Liver	Liver
12	chr3:53173200-53175000	Enhancers	Pancreas	Pancrea
13	chr3:53173200-53178000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:53173400-53175600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:53173600-53175400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:53173800-53174800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:53173800-53175200	Enhancers	Right Atrium	heart
18	chr3:53173800-53175400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:53174000-53175000	Enhancers	Gastric	stomach
20	chr3:53174000-53175600	Enhancers	Osteobl	bone
21	chr3:53174000-53182400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:53174200-53175200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:53174200-53175200	Enhancers	HepG2	liver
24	chr3:53174200-53175400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:53174200-53175400	Enhancers	K562	blood
26	chr3:53174200-53175600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:53174200-53175600	Enhancers	Adipose Nuclei	Adipose
28	chr3:53174200-53175600	Enhancers	Left Ventricle	heart
29	chr3:53174200-53175800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:53174200-53175800	Enhancers	NHLF	lung
31	chr3:53174200-53176200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:53174400-53174800	Enhancers	Brain Substantia Nigra	brain
33	chr3:53174400-53175000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:53174400-53175000	Enhancers	Esophagus	oesophagus
35	chr3:53174400-53175200	Enhancers	NH-A	brain
36	chr3:53174400-53175400	Enhancers	HMEC	breast
37	chr3:53174400-53175600	Enhancers	Lung	lung
38	chr3:53174400-53175600	Enhancers	Hela-S3	cervix
39	chr3:53174400-53175600	Enhancers	NHDF-Ad	bronchial
40	chr3:53174400-53175800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:53174400-53175800	Enhancers	Fetal Thymus	thymus
42	chr3:53174400-53176000	Enhancers	Primary hematopoietic stem cells	blood
43	chr3:53174400-53176000	Enhancers	Stomach Mucosa	stomach
44	chr3:53174400-53177000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr3:53174400-53178000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:53174600-53175000	Enhancers	Brain Hippocampus Middle	brain
47	chr3:53174600-53175000	Weak transcription	Fetal Heart	heart
48	chr3:53174600-53175400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:53174600-53175400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:53174600-53175400	Enhancers	HSMM	muscle

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