Variant report

Variant	rs57008939
Chromosome Location	chr3:52711370-52711371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10510759	0.83[AFR][1000 genomes]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs1987234	0.84[AFR][1000 genomes]
rs34173244	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35911561	0.87[AFR][1000 genomes]
rs35920544	0.83[AFR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56259931	0.84[AFR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57246324	0.84[AFR][1000 genomes]
rs57298447	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57319306	0.84[AFR][1000 genomes]
rs57560655	0.84[AFR][1000 genomes]
rs57757646	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58100002	0.84[AFR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs58725214	0.84[AFR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60415551	0.84[AFR][1000 genomes]
rs60611300	0.84[AFR][1000 genomes]
rs60682984	0.84[AFR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60823713	0.84[AFR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs60916588	0.84[AFR][1000 genomes]
rs61220667	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61538294	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes];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]
rs72947580	0.84[AFR][1000 genomes]
rs72947589	0.83[AFR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72965181	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7648016	0.81[AFR][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:127 , 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	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
6	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:52670800-52715400	Strong transcription	Dnd41	blood
8	chr3:52681200-52716200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:52688000-52714800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:52696000-52712000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:52696200-52711800	Weak transcription	Aorta	Aorta
12	chr3:52698800-52714400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:52699400-52715600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:52700600-52715000	Strong transcription	Primary B cells from cord blood	blood
15	chr3:52701800-52715600	Strong transcription	Brain Germinal Matrix	brain
16	chr3:52702000-52714400	Strong transcription	Fetal Lung	lung
17	chr3:52703600-52712200	Strong transcription	Liver	Liver
18	chr3:52703600-52716000	Strong transcription	Fetal Brain Female	brain
19	chr3:52703800-52713400	Strong transcription	Primary T cells from cord blood	blood
20	chr3:52703800-52715800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52704000-52712800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:52704000-52714200	Strong transcription	Thymus	Thymus
23	chr3:52704000-52714600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:52704000-52716000	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:52704400-52714000	Strong transcription	Fetal Intestine Large	intestine
26	chr3:52704600-52714200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:52704800-52715600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:52705000-52713000	Weak transcription	Right Atrium	heart
29	chr3:52705000-52714000	Strong transcription	Brain Anterior Caudate	brain
30	chr3:52705000-52714400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:52705200-52715200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:52705600-52714600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:52705600-52715000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:52705600-52715200	Strong transcription	Placenta	Placenta
35	chr3:52705600-52715800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52705800-52715600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:52706000-52714200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:52706000-52714400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:52706000-52715000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:52706000-52716200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:52706000-52716200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52706200-52713000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:52706200-52713000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:52706200-52714800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:52706200-52715800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:52706200-52715800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:52706400-52712000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:52706400-52712200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:52706400-52712200	Weak transcription	Gastric	stomach
50	chr3:52706400-52712200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links