Variant report

Variant	rs58476959
Chromosome Location	chr4:56362401-56362402
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10012559	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10034170	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1021306	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021307	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462028	0.82[ASN][1000 genomes]
rs10462033	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048004	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10529258	0.86[EUR][1000 genomes]
rs10866424	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732481	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11932595	0.93[ASN][1000 genomes]
rs11939971	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12505265	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12509047	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133077	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13134079	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488941	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1522109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546004	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721215	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17721497	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17722870	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17722979	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17779627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1801260	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1906676	0.85[EUR][1000 genomes]
rs1967078	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979604	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1979605	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070062	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2101476	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2130038	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2130040	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412658	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412659	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412661	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412662	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412664	0.87[ASN][1000 genomes]
rs34299771	0.84[ASN][1000 genomes]
rs3792603	0.86[ASN][1000 genomes]
rs3805156	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41324951	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4336288	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4865006	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865012	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865014	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55729020	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869433	1.00[ASN][1000 genomes]
rs55885973	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56056791	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56152424	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56196624	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57338268	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57826934	0.93[ASN][1000 genomes]
rs62303686	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62303690	0.86[ASN][1000 genomes]
rs62303691	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303692	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303708	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303709	0.86[ASN][1000 genomes]
rs62303711	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62303712	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62303713	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62303715	0.96[ASN][1000 genomes]
rs62303716	0.96[ASN][1000 genomes]
rs62303718	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62303722	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62303724	0.96[ASN][1000 genomes]
rs62303726	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303728	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303730	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303731	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303732	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305264	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305265	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305267	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305268	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305269	1.00[ASN][1000 genomes]
rs62305270	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305271	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309728	1.00[ASN][1000 genomes]
rs62309729	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309730	1.00[ASN][1000 genomes]
rs62309758	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62309759	0.95[ASN][1000 genomes]
rs62310862	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62310866	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554282	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554283	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554284	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554285	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554287	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554290	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6554291	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67963898	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822553	0.89[EUR][1000 genomes]
rs6828474	0.96[ASN][1000 genomes]
rs6830728	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6846764	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6848755	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6851971	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6853506	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6856004	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs716806	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73236140	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73236142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73236149	1.00[ASN][1000 genomes]
rs73236153	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7659095	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660668	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665286	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7665846	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676245	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7681414	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683997	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697067	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972446	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9993599	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][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:107 , 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	chr4:56314400-56377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:56318600-56363400	Weak transcription	HepG2	liver
6	chr4:56332600-56365600	Weak transcription	Esophagus	oesophagus
7	chr4:56332600-56377800	Weak transcription	Gastric	stomach
8	chr4:56336000-56376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:56337400-56377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:56341000-56363600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:56341400-56364200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:56341400-56365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:56341400-56385600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:56341600-56365800	Weak transcription	Lung	lung
15	chr4:56341600-56369200	Weak transcription	HSMMtube	muscle
16	chr4:56341600-56369400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:56341600-56377000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:56341800-56365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:56341800-56366600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:56341800-56376400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:56341800-56376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:56342200-56365600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:56342200-56377600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:56342400-56376600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:56342400-56378200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:56342600-56369200	Weak transcription	HMEC	breast
27	chr4:56342800-56364200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:56342800-56369200	Weak transcription	NH-A	brain
29	chr4:56342800-56391400	Weak transcription	Psoas Muscle	Psoas
30	chr4:56344600-56378200	Weak transcription	Brain Germinal Matrix	brain
31	chr4:56350400-56365800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:56350400-56365800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:56354400-56365400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:56354600-56372200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:56355200-56363000	Weak transcription	Brain Angular Gyrus	brain
36	chr4:56355200-56365600	Weak transcription	Primary T cells from cord blood	blood
37	chr4:56355400-56364400	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:56355400-56365600	Weak transcription	Liver	Liver
39	chr4:56355400-56369000	Weak transcription	NHEK	skin
40	chr4:56355400-56372800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:56355400-56373000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:56355400-56373200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:56355400-56374000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:56355400-56375000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:56355400-56377000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:56355400-56377000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:56355400-56377200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:56355400-56377400	Weak transcription	Brain Anterior Caudate	brain
49	chr4:56355400-56378000	Weak transcription	Aorta	Aorta
50	chr4:56355400-56379200	Weak transcription	Ovary	ovary

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