Variant report

Variant	rs1532520
Chromosome Location	chr5:58286244-58286245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10074854	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461657	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1463816	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498612	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553114	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159724	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1846369	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973451	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927661	0.93[EUR][1000 genomes]
rs2936190	0.86[EUR][1000 genomes]
rs2936199	0.89[EUR][1000 genomes]
rs2968006	0.86[EUR][1000 genomes]
rs2968013	0.89[EUR][1000 genomes]
rs2968014	0.88[EUR][1000 genomes]
rs2968015	0.88[EUR][1000 genomes]
rs2968017	0.94[EUR][1000 genomes]
rs2968021	0.97[EUR][1000 genomes]
rs3805553	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805554	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805556	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3805557	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412423	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4321723	0.89[EUR][1000 genomes]
rs457959	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4621516	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4629551	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4699930	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4699931	0.87[EUR][1000 genomes]
rs4700314	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6450496	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875727	0.88[EUR][1000 genomes]
rs702519	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs702523	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7712725	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713069	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713345	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7724713	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7737685	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][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	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

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58266000-58287600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:58268000-58288400	Weak transcription	Stomach Mucosa	stomach
3	chr5:58268200-58287200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:58268400-58287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:58268400-58294400	Weak transcription	NH-A	brain
6	chr5:58268800-58286600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:58268800-58286800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:58268800-58287200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:58268800-58287800	Weak transcription	Placenta	Placenta
10	chr5:58268800-58288800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:58268800-58294600	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:58270800-58292600	Weak transcription	Fetal Brain Male	brain
14	chr5:58270800-58295800	Weak transcription	Small Intestine	intestine
15	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:58271000-58287600	Weak transcription	Esophagus	oesophagus
17	chr5:58271000-58293600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:58271000-58294600	Weak transcription	Brain Angular Gyrus	brain
19	chr5:58271600-58287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:58271600-58294400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:58272800-58289000	Weak transcription	HUVEC	blood vessel
22	chr5:58273000-58294400	Weak transcription	Brain Anterior Caudate	brain
23	chr5:58273400-58289200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:58273800-58294400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:58276400-58288800	Strong transcription	Hela-S3	cervix
26	chr5:58276800-58286800	Strong transcription	Fetal Thymus	thymus
27	chr5:58277800-58295600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:58278400-58297400	Weak transcription	HSMMtube	muscle
29	chr5:58278400-58299000	Weak transcription	Gastric	stomach
30	chr5:58278600-58292200	Weak transcription	Brain Germinal Matrix	brain
31	chr5:58279000-58288600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:58279200-58288000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
34	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:58279600-58287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:58279600-58293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
38	chr5:58279800-58286800	Weak transcription	Colonic Mucosa	Colon
39	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:58280000-58287000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:58280200-58287200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:58280200-58297000	Weak transcription	Fetal Heart	heart
43	chr5:58280200-58297000	Weak transcription	Fetal Kidney	kidney
44	chr5:58280200-58297200	Weak transcription	Psoas Muscle	Psoas
45	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
46	chr5:58280400-58297600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:58281000-58288200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:58281200-58289200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:58281400-58288800	Strong transcription	HSMM	muscle
50	chr5:58281800-58287200	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links