Variant report

Variant	rs28494643
Chromosome Location	chr4:99290671-99290672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10001137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027340	0.87[EUR][1000 genomes]
rs17027388	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17027393	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	1.00[AMR][1000 genomes]
rs28497963	0.91[AMR][1000 genomes]
rs28503871	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705201	0.80[AMR][1000 genomes]
rs28731135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55993060	0.87[EUR][1000 genomes]
rs56805018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60281573	0.87[EUR][1000 genomes]
rs60544326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60638903	0.87[EUR][1000 genomes]
rs61485715	0.87[EUR][1000 genomes]
rs6831386	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832142	0.87[EUR][1000 genomes]
rs73832145	0.87[EUR][1000 genomes]
rs73832149	0.87[EUR][1000 genomes]
rs73832156	0.87[EUR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7656868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv999097	chr4:99271563-99304326	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1012360	chr4:99271563-99308481	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99215000-99317000	Weak transcription	Left Ventricle	heart
2	chr4:99262800-99295600	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:99262800-99333400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:99263000-99296000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:99264200-99338200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:99265200-99297800	Weak transcription	Osteobl	bone
7	chr4:99265400-99298400	Weak transcription	NHDF-Ad	bronchial
8	chr4:99271600-99314800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:99277200-99295400	Weak transcription	Brain Anterior Caudate	brain
10	chr4:99280000-99298600	Weak transcription	NHLF	lung
11	chr4:99285000-99337800	Weak transcription	HUVEC	blood vessel
12	chr4:99285200-99294000	Weak transcription	HMEC	breast
13	chr4:99285200-99306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:99286200-99291000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:99286400-99291000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:99286400-99310200	Weak transcription	Small Intestine	intestine
17	chr4:99287000-99290800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:99287000-99291000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:99288400-99342400	Weak transcription	A549	lung
20	chr4:99288600-99293200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:99288600-99295800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:99288600-99295800	Weak transcription	HSMMtube	muscle
23	chr4:99288600-99298600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:99288600-99313000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:99288800-99291600	Weak transcription	Fetal Thymus	thymus
26	chr4:99288800-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:99288800-99294600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:99288800-99295800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:99288800-99319800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:99288800-99329200	Weak transcription	Esophagus	oesophagus
31	chr4:99288800-99332000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr4:99288800-99333600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:99289000-99291200	Weak transcription	Thymus	Thymus
34	chr4:99289000-99291800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:99289000-99291800	Weak transcription	Fetal Stomach	stomach
36	chr4:99289000-99292400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:99289000-99292600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:99289000-99294400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:99289000-99295600	Weak transcription	NHEK	skin
40	chr4:99289000-99298000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:99289000-99298400	Strong transcription	Dnd41	blood
42	chr4:99289000-99301000	Weak transcription	Liver	Liver
43	chr4:99289000-99313600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:99289000-99314600	Weak transcription	Lung	lung
45	chr4:99289000-99318400	Weak transcription	Ovary	ovary
46	chr4:99289000-99333000	Weak transcription	Fetal Intestine Large	intestine
47	chr4:99289000-99333400	Weak transcription	Pancreas	Pancrea
48	chr4:99289000-99333600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:99289200-99291000	Strong transcription	HSMM	muscle
50	chr4:99289400-99293400	Weak transcription	Aorta	Aorta

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