Variant report

Variant	rs539713404
Chromosome Location	chr2:99552556-99552557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99523789..99526225-chr2:99550557..99552954,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3339215	chr2:99550420-99554818	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3412425	chr2:99551545-99553993	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99549400-99553800	Active TSS	Brain Anterior Caudate	brain
2	chr2:99550000-99553800	Active TSS	Brain Angular Gyrus	brain
3	chr2:99550800-99553200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:99551200-99553800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99551200-99554000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:99551400-99553800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr2:99551600-99552800	Bivalent/Poised TSS	Right Ventricle	heart
8	chr2:99551800-99553000	Bivalent/Poised TSS	HUVEC	blood vessel
9	chr2:99551800-99553200	Active TSS	Ovary	ovary
10	chr2:99551800-99553600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:99551800-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:99551800-99553800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr2:99551800-99553800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:99551800-99554000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:99551800-99554000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:99552000-99552600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
17	chr2:99552000-99552600	Bivalent Enhancer	Fetal Brain Male	brain
18	chr2:99552000-99552600	Bivalent Enhancer	Left Ventricle	heart
19	chr2:99552000-99552800	Active TSS	Rectal Smooth Muscle	rectum
20	chr2:99552000-99553000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:99552000-99553000	Active TSS	Aorta	Aorta
22	chr2:99552000-99553000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
23	chr2:99552000-99553000	Bivalent/Poised TSS	HSMMtube	muscle
24	chr2:99552000-99553200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
25	chr2:99552000-99553200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr2:99552000-99553200	Bivalent/Poised TSS	Osteobl	bone
27	chr2:99552000-99553400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr2:99552000-99553600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:99552000-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:99552000-99553600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:99552000-99553600	Bivalent/Poised TSS	Psoas Muscle	Psoas
32	chr2:99552000-99553600	Active TSS	Right Atrium	heart
33	chr2:99552000-99553800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:99552000-99553800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr2:99552000-99553800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:99552000-99553800	Active TSS	Gastric	stomach
37	chr2:99552200-99552600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr2:99552200-99552600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:99552200-99552600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:99552200-99552800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:99552200-99552800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:99552200-99553000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:99552200-99553000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:99552200-99553000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:99552200-99553000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr2:99552200-99553000	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:99552200-99553000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:99552200-99553000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:99552200-99553000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:99552200-99553000	Bivalent/Poised TSS	Fetal Stomach	stomach

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