Variant report

Variant	rs73825141
Chromosome Location	chr3:28394916-28394917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:28388560-28395839	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:28387839-28396035	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:28394701-28395752	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28388985..28391534-chr3:28392522..28395411,2	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000163512	Chromatin interaction
ENSG00000206559	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11916224	0.90[AFR][1000 genomes]
rs55962685	0.98[AFR][1000 genomes]
rs60023459	0.90[AFR][1000 genomes]
rs61588415	0.90[AFR][1000 genomes]
rs6804419	0.98[AFR][1000 genomes]
rs73822579	0.85[AFR][1000 genomes]
rs73825125	0.90[AFR][1000 genomes]
rs73825129	0.90[AFR][1000 genomes]
rs73825132	0.90[AFR][1000 genomes]
rs73825133	0.90[AFR][1000 genomes]
rs73825137	0.90[AFR][1000 genomes]
rs73825138	0.90[AFR][1000 genomes]
rs7628073	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28391200-28395200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:28391400-28395200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:28391400-28395200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:28391400-28396000	Weak transcription	Colonic Mucosa	Colon
5	chr3:28391600-28395400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:28391600-28395400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:28391600-28397800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:28391600-28398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:28391800-28395000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:28391800-28395200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:28391800-28395200	Weak transcription	Osteobl	bone
12	chr3:28391800-28395400	Weak transcription	Brain Angular Gyrus	brain
13	chr3:28391800-28395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:28391800-28397000	Weak transcription	HSMMtube	muscle
15	chr3:28392000-28395000	Weak transcription	NHDF-Ad	bronchial
16	chr3:28392000-28397200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:28392200-28395400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:28392200-28395800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:28392400-28395000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:28392400-28395400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:28392600-28395400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:28392800-28395600	ZNF genes & repeats	Fetal Lung	lung
23	chr3:28392800-28395800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:28392800-28395800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr3:28392800-28395800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:28393000-28395000	Weak transcription	Psoas Muscle	Psoas
27	chr3:28393000-28395400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:28393000-28395800	Weak transcription	Dnd41	blood
29	chr3:28393200-28395000	ZNF genes & repeats	Ovary	ovary
30	chr3:28393200-28395600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr3:28393200-28395600	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr3:28393200-28395600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr3:28393200-28395600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:28393200-28395800	ZNF genes & repeats	Liver	Liver
35	chr3:28393200-28395800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr3:28393400-28395400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:28393400-28395600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
38	chr3:28393800-28395600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:28393800-28395600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
40	chr3:28393800-28412200	Weak transcription	Pancreas	Pancrea
41	chr3:28394000-28395000	Weak transcription	HSMM	muscle
42	chr3:28394000-28395200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:28394000-28395200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:28394400-28395200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:28394400-28395600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr3:28394400-28395600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr3:28394600-28395600	Strong transcription	Left Ventricle	heart
48	chr3:28394600-28396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:28394800-28395600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr3:28394800-28395600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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