Variant report

Variant	rs73839116
Chromosome Location	chr3:52652550-52652551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52642946..52645820-chr3:52652217..52653934,2	K562	blood:
2	chr3:52651699..52653364-chr3:52664057..52666532,2	K562	blood:
3	chr3:52652235..52654502-chr3:52681083..52683381,2	K562	blood:
4	chr3:52651986..52653955-chr3:52666537..52669431,2	K562	blood:

Variant related genes	Relation type
ENSG00000163939	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17052401	0.89[AFR][1000 genomes]
rs55971019	1.00[AMR][1000 genomes]
rs56898787	1.00[AMR][1000 genomes]
rs56961704	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60499166	1.00[AMR][1000 genomes]
rs60997031	1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes]
rs6766038	1.00[AMR][1000 genomes]
rs6803509	0.89[AFR][1000 genomes]
rs73837599	1.00[AMR][1000 genomes]
rs73839117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839182	0.89[AFR][1000 genomes]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52634800-52654400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52634800-52654400	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:52634800-52686000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr3:52635600-52654200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:52635600-52655200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52635800-52654400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:52635800-52654600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:52635800-52654600	Strong transcription	Adipose Nuclei	Adipose
12	chr3:52635800-52657800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:52636000-52653200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52636000-52653200	Strong transcription	Fetal Intestine Large	intestine
15	chr3:52636000-52654400	Strong transcription	Fetal Thymus	thymus
16	chr3:52636000-52655200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:52636000-52703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:52636000-52704000	Strong transcription	Placenta	Placenta
19	chr3:52636200-52653600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:52636200-52703200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:52636400-52654600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:52636600-52654800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:52636600-52669200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:52636600-52673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52636600-52677400	Weak transcription	Pancreas	Pancrea
26	chr3:52636800-52652800	Strong transcription	Fetal Brain Female	brain
27	chr3:52636800-52654600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:52636800-52654800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:52636800-52662800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:52636800-52703600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:52637400-52654200	Strong transcription	Primary T cells from cord blood	blood
33	chr3:52637800-52654200	Strong transcription	Thymus	Thymus
34	chr3:52638800-52658400	Weak transcription	Esophagus	oesophagus
35	chr3:52639600-52670000	Strong transcription	Dnd41	blood
36	chr3:52640200-52655800	Weak transcription	Lung	lung
37	chr3:52640600-52663200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:52640800-52652600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:52640800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52641000-52670800	Weak transcription	Stomach Mucosa	stomach
41	chr3:52641200-52654600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52641400-52654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52641600-52654600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:52641600-52664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:52641800-52652600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52641800-52653800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:52642200-52657600	Weak transcription	Brain Angular Gyrus	brain
48	chr3:52642400-52652600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:52642400-52652600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:52642400-52671000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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