Variant report

Variant	rs11725439
Chromosome Location	chr4:56358331-56358332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11722277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11722415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11723580	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11724300	1.00[AFR][1000 genomes]
rs11725081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725738	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727248	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729403	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11732078	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11732684	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs11733959	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11733966	1.00[AFR][1000 genomes]
rs11735654	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1522113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085763	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs28409498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28450557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34897046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35133040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35793438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
3	chr4:56304800-56375800	Weak transcription	Pancreas	Pancrea
4	chr4:56306000-56361200	Weak transcription	Stomach Mucosa	stomach
5	chr4:56314400-56377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:56318600-56363400	Weak transcription	HepG2	liver
7	chr4:56318800-56358400	Weak transcription	Right Ventricle	heart
8	chr4:56332600-56365600	Weak transcription	Esophagus	oesophagus
9	chr4:56332600-56377800	Weak transcription	Gastric	stomach
10	chr4:56336000-56376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:56337400-56377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:56341000-56363600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:56341400-56364200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:56341400-56365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:56341400-56385600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:56341600-56358600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:56341600-56365800	Weak transcription	Lung	lung
18	chr4:56341600-56369200	Weak transcription	HSMMtube	muscle
19	chr4:56341600-56369400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:56341600-56377000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:56341800-56360400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:56341800-56361000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:56341800-56365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:56341800-56366600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:56341800-56376400	Weak transcription	Brain Substantia Nigra	brain
26	chr4:56341800-56376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:56342200-56365600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:56342200-56377600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:56342400-56376600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:56342400-56378200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:56342600-56369200	Weak transcription	HMEC	breast
32	chr4:56342800-56364200	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:56342800-56369200	Weak transcription	NH-A	brain
34	chr4:56342800-56391400	Weak transcription	Psoas Muscle	Psoas
35	chr4:56344600-56378200	Weak transcription	Brain Germinal Matrix	brain
36	chr4:56345000-56360400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:56346800-56360400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:56347200-56360800	Weak transcription	Fetal Intestine Small	intestine
39	chr4:56350400-56365800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:56350400-56365800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:56354400-56365400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:56354600-56372200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:56355000-56360600	Weak transcription	Primary B cells from cord blood	blood
44	chr4:56355200-56360400	Weak transcription	Adipose Nuclei	Adipose
45	chr4:56355200-56363000	Weak transcription	Brain Angular Gyrus	brain
46	chr4:56355200-56365600	Weak transcription	Primary T cells from cord blood	blood
47	chr4:56355400-56360200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:56355400-56360200	Weak transcription	Left Ventricle	heart
49	chr4:56355400-56360400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:56355400-56360400	Weak transcription	Fetal Muscle Leg	muscle

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