Variant report

Variant	rs28539646
Chromosome Location	chr5:58428720-58428721
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10036199	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10056754	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10058671	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10058676	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10062176	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10069146	0.88[EUR][1000 genomes]
rs17722929	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960	1.00[ASN][1000 genomes]
rs28544243	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35425879	0.87[EUR][1000 genomes]
rs72764076	0.84[EUR][1000 genomes]
rs72764077	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764078	1.00[ASN][1000 genomes]
rs7734053	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7734070	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58423800-58429400	Weak transcription	Aorta	Aorta
2	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
3	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:58424200-58429400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:58424200-58429400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:58424200-58429400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:58424200-58429400	Weak transcription	Left Ventricle	heart
8	chr5:58424200-58429400	Weak transcription	Psoas Muscle	Psoas
9	chr5:58424200-58429400	Weak transcription	HMEC	breast
10	chr5:58424200-58432800	Weak transcription	Right Ventricle	heart
11	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
12	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:58424400-58430200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58424400-58431400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:58424600-58429400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:58424600-58429600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:58424800-58429000	Weak transcription	NHDF-Ad	bronchial
18	chr5:58424800-58429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:58424800-58429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:58424800-58429400	Weak transcription	Right Atrium	heart
21	chr5:58424800-58429600	Weak transcription	HSMM	muscle
22	chr5:58425000-58429600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:58425000-58429600	Weak transcription	Osteobl	bone
24	chr5:58425200-58429400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:58425200-58429400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:58425400-58429400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:58425600-58429400	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:58425600-58429400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:58425800-58429800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:58426600-58430200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:58426800-58429400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr5:58426800-58430200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:58426800-58431200	Enhancers	Primary T cells from cord blood	blood
34	chr5:58427200-58429200	Weak transcription	Hela-S3	cervix
35	chr5:58427200-58429400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:58427200-58429400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:58427400-58429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:58427400-58430000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:58427600-58428800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:58428000-58431000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr5:58428400-58428800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr5:58428400-58429600	Enhancers	A549	lung
44	chr5:58428600-58428800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr5:58428600-58428800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr5:58428600-58428800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links