Variant report

Variant	rs28662393
Chromosome Location	chr3:113044826-113044827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10934229	0.80[ASN][1000 genomes]
rs10934230	0.80[ASN][1000 genomes]
rs12630518	0.83[ASN][1000 genomes]
rs12634060	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12634440	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636959	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637924	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13318454	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16860850	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860868	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16860899	0.87[ASN][1000 genomes]
rs17882622	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270781	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34965320	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682133	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682137	0.82[ASN][1000 genomes]
rs4682485	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55667700	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55748551	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55757335	0.83[ASN][1000 genomes]
rs55973292	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438138	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438142	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6801184	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809516	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73235041	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73235059	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235065	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235066	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73235068	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73235093	0.80[AMR][1000 genomes]
rs73237104	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73237110	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73237123	0.87[ASN][1000 genomes]
rs73237130	0.84[ASN][1000 genomes]
rs73237143	0.83[ASN][1000 genomes]
rs73239107	0.83[ASN][1000 genomes]
rs763805	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8179926	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9820386	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9822309	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842039	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9844111	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847084	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852204	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857414	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863193	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878805	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
3	chr3:113024600-113046600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:113024600-113081000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:113028600-113053400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:113034400-113046800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:113034800-113048400	Weak transcription	Fetal Lung	lung
8	chr3:113034800-113053600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:113034800-113054000	Weak transcription	Psoas Muscle	Psoas
10	chr3:113035000-113050800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:113035000-113052000	Weak transcription	HSMMtube	muscle
12	chr3:113035000-113053000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:113035400-113045000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:113035400-113052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:113035800-113046400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:113036400-113053400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:113036400-113055600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:113036600-113049800	Weak transcription	Fetal Intestine Large	intestine
19	chr3:113036600-113051000	Weak transcription	Thymus	Thymus
20	chr3:113036600-113081000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:113036800-113046000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:113036800-113050000	Weak transcription	Right Ventricle	heart
23	chr3:113036800-113050400	Weak transcription	Lung	lung
24	chr3:113036800-113065600	Weak transcription	Aorta	Aorta
25	chr3:113036800-113073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:113036800-113081000	Weak transcription	Gastric	stomach
27	chr3:113036800-113088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:113037000-113053600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:113037800-113065600	Weak transcription	HSMM	muscle
30	chr3:113042000-113046200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:113042000-113080800	Weak transcription	Ovary	ovary
32	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
33	chr3:113042400-113059800	Weak transcription	Pancreas	Pancrea
34	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:113043400-113045200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr3:113043600-113046200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:113043800-113046200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:113043800-113065600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:113044400-113045400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:113044400-113047000	Weak transcription	Fetal Heart	heart
41	chr3:113044600-113045200	Strong transcription	Primary T cells from cord blood	blood
42	chr3:113044600-113045200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:113044600-113045200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:113044600-113045400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:113044600-113045400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:113044600-113045400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr3:113044600-113045400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:113044600-113045400	Strong transcription	Adipose Nuclei	Adipose
49	chr3:113044600-113045400	Strong transcription	Liver	Liver
50	chr3:113044600-113045400	Strong transcription	Brain Anterior Caudate	brain

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