Variant report

Variant	rs58897996
Chromosome Location	chr5:14358043-14358044
allele	C/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:53)

rs_ID	r²[population]
rs10062034	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10076925	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16903350	0.83[AMR][1000 genomes]
rs16903399	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16903467	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55750919	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55754427	1.00[AMR][1000 genomes]
rs55773296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56114434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56141029	1.00[AMR][1000 genomes]
rs56227025	1.00[AMR][1000 genomes]
rs56664186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56712870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57560019	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57974400	1.00[AMR][1000 genomes]
rs58324829	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58443103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58716074	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59499572	0.83[AMR][1000 genomes]
rs59853866	1.00[AMR][1000 genomes]
rs60077210	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568524	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61180647	0.83[AMR][1000 genomes]
rs61396062	1.00[AMR][1000 genomes]
rs61509800	0.83[AMR][1000 genomes]
rs6868596	0.83[AMR][1000 genomes]
rs73748806	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73748810	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73748811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749083	1.00[AMR][1000 genomes]
rs73749085	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749234	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749235	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73751307	0.83[AMR][1000 genomes]
rs73751311	0.83[AMR][1000 genomes]
rs73751318	0.83[AMR][1000 genomes]
rs73751322	1.00[AMR][1000 genomes]
rs73751323	1.00[AMR][1000 genomes]
rs73751327	0.83[AMR][1000 genomes]
rs73751329	1.00[AMR][1000 genomes]
rs73751335	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73751336	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73751337	1.00[AMR][1000 genomes]
rs73751338	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73751339	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73751340	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7703674	0.83[AMR][1000 genomes]
rs7705426	0.83[AMR][1000 genomes]
rs7713114	0.83[AMR][1000 genomes]
rs7716460	1.00[AMR][1000 genomes]
rs7723309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7724084	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
2	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
4	chr5:14341400-14359400	Weak transcription	Primary T cells from cord blood	blood
5	chr5:14342600-14358200	Weak transcription	Pancreas	Pancrea
6	chr5:14342800-14365200	Weak transcription	Small Intestine	intestine
7	chr5:14343200-14358800	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:14343800-14362400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:14347000-14358800	Weak transcription	Fetal Lung	lung
10	chr5:14348600-14359800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:14348800-14358600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:14349000-14358200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:14349400-14360000	Weak transcription	Fetal Kidney	kidney
14	chr5:14350400-14358800	Weak transcription	HMEC	breast
15	chr5:14350400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:14352200-14358200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:14353600-14366200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:14353600-14385200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr5:14354200-14358400	Weak transcription	Hela-S3	cervix
22	chr5:14354400-14374800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:14354600-14402400	Strong transcription	Liver	Liver
24	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
25	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr5:14355400-14365200	Strong transcription	HSMM	muscle
27	chr5:14355600-14375000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:14355800-14358800	Weak transcription	NHDF-Ad	bronchial
29	chr5:14355800-14359000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:14356000-14362400	Strong transcription	Osteobl	bone
31	chr5:14356000-14366200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr5:14356400-14358400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:14356400-14365400	Strong transcription	NHEK	skin
34	chr5:14356400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:14356600-14363800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:14356600-14365200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:14356800-14358200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:14356800-14358200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:14356800-14358600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:14356800-14358600	Enhancers	Right Atrium	heart
41	chr5:14356800-14370200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:14356800-14376000	Strong transcription	HepG2	liver
43	chr5:14357000-14358200	Enhancers	Left Ventricle	heart
44	chr5:14357000-14358400	Enhancers	Fetal Brain Male	brain
45	chr5:14357000-14358400	Genic enhancers	Fetal Muscle Leg	muscle
46	chr5:14357000-14358400	Weak transcription	GM12878-XiMat	blood
47	chr5:14357000-14358600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:14357000-14359600	Enhancers	Fetal Heart	heart
49	chr5:14357000-14360000	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr5:14357000-14370400	Strong transcription	Fetal Intestine Small	intestine

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