Variant report

Variant	rs58620246
Chromosome Location	chr5:108321371-108321372
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11953198	0.93[ASN][1000 genomes]
rs17161573	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161574	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797817	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797822	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851456	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56134914	0.93[ASN][1000 genomes]
rs56381733	1.00[ASN][1000 genomes]
rs56792678	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57158292	0.93[ASN][1000 genomes]
rs58642014	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58834152	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59055229	1.00[ASN][1000 genomes]
rs59699586	0.81[ASN][1000 genomes]
rs59923567	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60094908	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60144513	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61090818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61155278	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61640970	0.93[ASN][1000 genomes]
rs6594344	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66485253	0.93[ASN][1000 genomes]
rs66834040	0.93[ASN][1000 genomes]
rs67145801	0.93[ASN][1000 genomes]
rs67156774	0.93[ASN][1000 genomes]
rs67338203	1.00[ASN][1000 genomes]
rs6872912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793930	0.93[ASN][1000 genomes]
rs73209329	0.93[ASN][1000 genomes]
rs73209333	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73209338	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73209345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73209347	0.93[ASN][1000 genomes]
rs73209352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73209366	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73211525	0.93[ASN][1000 genomes]
rs73211537	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73211547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73211557	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73211567	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211584	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73211589	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73211590	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73211596	1.00[EUR][1000 genomes]
rs73213504	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73780769	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7713828	0.93[ASN][1000 genomes]
rs7715534	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7723264	0.93[ASN][1000 genomes]
rs7723604	0.93[ASN][1000 genomes]
rs7723612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7723644	0.93[ASN][1000 genomes]
rs7736915	0.93[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	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
3	chr5:108277600-108322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:108279200-108325600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:108282200-108324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:108282400-108327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:108290000-108322000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:108290000-108328800	Weak transcription	Esophagus	oesophagus
9	chr5:108293400-108325600	Weak transcription	NHEK	skin
10	chr5:108294400-108329400	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:108299600-108328800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:108301400-108328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
14	chr5:108302200-108330200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:108303000-108329000	Weak transcription	Gastric	stomach
16	chr5:108303200-108322200	Weak transcription	Pancreas	Pancrea
17	chr5:108303200-108322400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:108303200-108331800	Weak transcription	Ovary	ovary
19	chr5:108303800-108322000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:108303800-108322200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:108304000-108328800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:108308400-108328800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:108308400-108336000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:108309800-108333600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:108310000-108323400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:108310200-108322400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:108310200-108322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:108310400-108322400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:108313200-108322400	Weak transcription	Psoas Muscle	Psoas
30	chr5:108314200-108329400	Weak transcription	Adipose Nuclei	Adipose
31	chr5:108317600-108322400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:108317800-108329200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:108319000-108325600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:108319200-108321800	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:108319600-108325400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:108319600-108325600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:108319800-108325200	Weak transcription	NHDF-Ad	bronchial
38	chr5:108319800-108340800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:108320000-108335000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:108321000-108321600	Strong transcription	Fetal Lung	lung
41	chr5:108321200-108321400	ZNF genes & repeats	Lung	lung
42	chr5:108321200-108321600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:108321200-108321600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr5:108321200-108321600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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