Variant report

Variant	rs16880875
Chromosome Location	chr5:52394990-52394991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52392231..52395065-chr5:52398498..52400912,2	K562	blood:
2	chr5:52384559..52387537-chr5:52393582..52396762,3	MCF-7	breast:
3	chr5:52388236..52391143-chr5:52394703..52396954,3	K562	blood:
4	chr5:52391585..52394108-chr5:52394132..52397970,3	K562	blood:

Variant related genes	Relation type
ENSG00000272123	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12515434	0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2233209	1.00[EUR][1000 genomes]
rs2910977	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3212517	0.83[EUR][1000 genomes]
rs3212519	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3212578	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3212623	0.86[EUR][1000 genomes]
rs3212632	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62359375	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62359376	0.92[AFR][1000 genomes];0.98[EUR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:52341200-52396400	Strong transcription	HMEC	breast
3	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
5	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
6	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:52385800-52395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:52388000-52395000	Weak transcription	Lung	lung
14	chr5:52388200-52398400	Strong transcription	HUVEC	blood vessel
15	chr5:52388400-52396200	Weak transcription	Hela-S3	cervix
16	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:52389600-52395000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:52390000-52397600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:52390600-52396200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:52390600-52397200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:52390600-52399600	Strong transcription	NHEK	skin
23	chr5:52390600-52401200	Strong transcription	Dnd41	blood
24	chr5:52390800-52396400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr5:52390800-52403800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52391000-52395600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:52391000-52401000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr5:52391000-52403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:52391400-52395000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:52391600-52403200	Weak transcription	Fetal Heart	heart
31	chr5:52392000-52404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:52392200-52400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:52392200-52401200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr5:52392400-52398600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:52392400-52400000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:52392400-52400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:52392400-52401400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:52392400-52403000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:52392400-52403400	Strong transcription	Liver	Liver
40	chr5:52392400-52404800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr5:52392600-52396000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:52392600-52400400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr5:52392800-52395400	Strong transcription	Aorta	Aorta
44	chr5:52392800-52395600	Strong transcription	Thymus	Thymus
45	chr5:52392800-52395800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:52392800-52396400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:52392800-52397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:52392800-52397000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:52392800-52399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:52392800-52400200	Strong transcription	Rectal Mucosa Donor 29	rectum

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