Variant report

Variant	rs558363833
Chromosome Location	chr19:52905319-52905320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52899758..52902696-chr19:52903314..52905986,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269834	Chromatin interaction
ENSG00000167555	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv978840	chr19:52905026-52909427	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52901800-52905400	Weak transcription	Thymus	Thymus
2	chr19:52901800-52907000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
3	chr19:52901800-52912600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:52902000-52905400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:52902000-52905600	Weak transcription	Stomach Mucosa	stomach
6	chr19:52902000-52906200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:52902000-52906400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:52902000-52908000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:52902000-52908800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:52902000-52913800	Weak transcription	Fetal Heart	heart
11	chr19:52902200-52905400	Weak transcription	Osteobl	bone
12	chr19:52902200-52906600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
13	chr19:52902200-52907400	Weak transcription	NHEK	skin
14	chr19:52902200-52908800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:52902200-52909200	Strong transcription	Placenta	Placenta
16	chr19:52902200-52909800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:52902200-52913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:52902200-52917400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:52902200-52919200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:52902400-52910400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:52902400-52913400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:52902400-52913400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:52902400-52917600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:52902600-52906400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:52902600-52906400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:52902600-52906600	Strong transcription	Primary T cells from cord blood	blood
27	chr19:52902600-52906800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:52902600-52907200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:52902600-52908200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:52902600-52910400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
31	chr19:52902600-52913000	Strong transcription	Fetal Stomach	stomach
32	chr19:52902600-52913600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:52902600-52914000	ZNF genes & repeats	Lung	lung
34	chr19:52902600-52917600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:52902600-52918200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:52902800-52906400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:52902800-52906600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr19:52902800-52912800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:52902800-52913400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:52902800-52914000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:52902800-52914200	Strong transcription	Brain Anterior Caudate	brain
42	chr19:52902800-52914200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:52902800-52915600	Strong transcription	HSMMtube	muscle
44	chr19:52902800-52924200	ZNF genes & repeats	Liver	Liver
45	chr19:52903000-52907200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:52903000-52911800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
47	chr19:52903000-52913000	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:52903000-52913600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr19:52903000-52913600	Strong transcription	Brain Hippocampus Middle	brain
50	chr19:52903000-52914000	ZNF genes & repeats	Ovary	ovary

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