Variant report

Variant	rs58779089
Chromosome Location	chr5:58323933-58323934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10052704	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10053177	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10061320	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10063703	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065498	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10067196	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069187	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940638	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11750426	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11948356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957827	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13357540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361043	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13362239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888990	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16888998	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1874857	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874858	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874859	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055296	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055297	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055298	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291851	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291852	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4279300	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4469166	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631140	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699932	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700315	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700317	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58940834	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61511922	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62358484	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62358490	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62358491	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62358492	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876057	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6888474	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7714489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7729722	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735570	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
2	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
4	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:58313000-58333400	Weak transcription	Lung	lung
6	chr5:58313200-58325600	Weak transcription	Fetal Lung	lung
7	chr5:58313200-58330200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:58315000-58325800	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58317200-58331600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:58317400-58325200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:58317800-58331800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:58318000-58333000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:58318400-58330600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:58318600-58330400	Weak transcription	Right Ventricle	heart
15	chr5:58318600-58330600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:58318600-58333000	Weak transcription	Left Ventricle	heart
17	chr5:58318600-58333200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:58319200-58324200	Weak transcription	Hela-S3	cervix
19	chr5:58320000-58326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:58320200-58334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:58320400-58324400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:58321600-58324000	Strong transcription	HSMM	muscle
23	chr5:58321600-58324600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:58321600-58326800	Strong transcription	Fetal Thymus	thymus
25	chr5:58321800-58325600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:58321800-58330200	Weak transcription	Osteobl	bone
27	chr5:58321800-58334000	Weak transcription	Gastric	stomach
28	chr5:58322000-58330200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:58322000-58331800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:58322200-58330400	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:58322200-58330600	Weak transcription	HSMMtube	muscle
32	chr5:58322400-58325600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:58322400-58330000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:58322400-58330600	Weak transcription	Right Atrium	heart
35	chr5:58322400-58330800	Weak transcription	HepG2	liver
36	chr5:58322600-58324000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:58322600-58324400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:58322800-58324200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:58323000-58324000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr5:58323000-58329200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:58323200-58325800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:58323200-58326600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:58323200-58330600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:58323400-58324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:58323400-58324200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:58323400-58324600	Strong transcription	Primary T cells from cord blood	blood
47	chr5:58323400-58324600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr5:58323400-58324800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:58323400-58326200	ZNF genes & repeats	A549	lung
50	chr5:58323400-58326400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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