Variant report

Variant	rs7648016
Chromosome Location	chr3:52614410-52614411
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:41)

rs_ID	r²[population]
rs10510759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.81[AFR][1000 genomes]
rs56259931	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.81[AFR][1000 genomes]
rs57246324	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.85[AMR][1000 genomes]
rs61538294	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.84[AFR][1000 genomes]
rs72947580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.82[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.96[AFR][1000 genomes];1.00[AMR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:52576800-52625600	Strong transcription	Fetal Thymus	thymus
4	chr3:52578200-52625600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:52585800-52627400	Weak transcription	Fetal Heart	heart
6	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:52594400-52614800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:52595200-52631000	Weak transcription	Stomach Mucosa	stomach
11	chr3:52596000-52622800	Weak transcription	K562	blood
12	chr3:52596000-52624200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:52598200-52625200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52600600-52615400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:52602200-52617400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:52602200-52623400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52602600-52624400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:52603200-52617400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:52603400-52625400	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:52603600-52623800	Strong transcription	Liver	Liver
21	chr3:52603800-52616000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:52603800-52625400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:52604000-52623400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:52606000-52615600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:52606000-52623400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:52606200-52625400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:52606400-52623600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:52606600-52623800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:52606600-52625400	Strong transcription	Dnd41	blood
30	chr3:52606800-52615200	Strong transcription	HSMM	muscle
31	chr3:52606800-52615800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:52606800-52623600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:52607000-52614800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:52607000-52615200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:52607200-52623600	Strong transcription	Primary T cells from cord blood	blood
36	chr3:52607400-52623200	Strong transcription	Left Ventricle	heart
37	chr3:52607600-52616000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:52607600-52618000	Strong transcription	Osteobl	bone
39	chr3:52607600-52623400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:52607600-52623800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:52607600-52623800	Strong transcription	Brain Germinal Matrix	brain
42	chr3:52607800-52614800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr3:52607800-52616200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:52607800-52619000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:52607800-52623600	Strong transcription	Adipose Nuclei	Adipose
46	chr3:52607800-52623800	Strong transcription	Placenta	Placenta
47	chr3:52607800-52626600	Strong transcription	Fetal Stomach	stomach
48	chr3:52608000-52621000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:52608200-52615600	Strong transcription	NH-A	brain
50	chr3:52608200-52621200	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links