Variant report

Variant	rs58409398
Chromosome Location	chr3:52634523-52634524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs56960576	1.00[AMR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60830326	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	1.00[EUR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73837804	1.00[AMR][1000 genomes]
rs73839126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52612000-52634800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:52612800-52634800	Weak transcription	A549	lung
6	chr3:52613400-52635000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:52613400-52635000	Weak transcription	Fetal Brain Male	brain
8	chr3:52613600-52634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:52613600-52635200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:52613600-52635200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52613600-52635200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:52614200-52634800	Weak transcription	Small Intestine	intestine
13	chr3:52620600-52634800	Weak transcription	Aorta	Aorta
14	chr3:52620800-52634800	Weak transcription	Esophagus	oesophagus
15	chr3:52620800-52635000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:52620800-52635000	Weak transcription	NHEK	skin
17	chr3:52621600-52635800	Weak transcription	Hela-S3	cervix
18	chr3:52622200-52635000	Weak transcription	Ovary	ovary
19	chr3:52623000-52635200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:52623200-52634800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:52623200-52635400	Weak transcription	HMEC	breast
22	chr3:52623400-52634600	Weak transcription	Fetal Kidney	kidney
23	chr3:52623400-52635000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:52623600-52634800	Weak transcription	NHDF-Ad	bronchial
25	chr3:52623600-52635000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52626200-52634800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:52626800-52634600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:52627400-52634600	Strong transcription	Placenta	Placenta
29	chr3:52627400-52634800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:52627800-52640600	Weak transcription	Fetal Heart	heart
31	chr3:52628000-52634600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:52628000-52634600	Strong transcription	HSMM	muscle
33	chr3:52628200-52634800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:52628200-52635200	Weak transcription	Psoas Muscle	Psoas
35	chr3:52628400-52635000	Strong transcription	Dnd41	blood
36	chr3:52628600-52640200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr3:52629600-52635600	Weak transcription	NH-A	brain
38	chr3:52630600-52634600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:52630800-52638600	Strong transcription	Osteobl	bone
40	chr3:52631200-52634600	Weak transcription	Pancreas	Pancrea
41	chr3:52631200-52634600	Weak transcription	Spleen	Spleen
42	chr3:52631200-52634600	Weak transcription	HSMMtube	muscle
43	chr3:52631200-52634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52631200-52634800	Weak transcription	Lung	lung
45	chr3:52631200-52635200	Weak transcription	Colonic Mucosa	Colon
46	chr3:52631200-52635200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:52631200-52635200	Weak transcription	NHLF	lung
48	chr3:52631400-52634600	Weak transcription	Left Ventricle	heart
49	chr3:52631400-52635000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:52631400-52635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links