Variant report

Variant	rs58100002
Chromosome Location	chr3:52589840-52589841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52588842..52591237-chr3:52592421..52595221,3	K562	blood:

Variant related genes	Relation type
ENSG00000221518	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv8459	chr3:52589746-52589924	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
6	chr3:52573600-52598400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:52574600-52594200	Weak transcription	K562	blood
9	chr3:52574600-52598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:52574800-52605000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:52576000-52590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:52576800-52625600	Strong transcription	Fetal Thymus	thymus
13	chr3:52577000-52599000	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:52577200-52599000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:52577600-52595400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:52577600-52598600	Strong transcription	Placenta	Placenta
17	chr3:52577600-52605200	Strong transcription	Dnd41	blood
18	chr3:52578000-52595400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:52578200-52591200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:52578200-52625600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:52578400-52598600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:52578400-52600600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:52578800-52598200	Strong transcription	Primary B cells from cord blood	blood
24	chr3:52578800-52598800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:52578800-52599600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:52578800-52601400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:52579000-52598600	Strong transcription	Thymus	Thymus
28	chr3:52579000-52599200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:52579200-52598200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:52580400-52590000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:52580400-52598400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:52580600-52590800	Strong transcription	Fetal Intestine Large	intestine
33	chr3:52580600-52598400	Strong transcription	Primary T cells from cord blood	blood
34	chr3:52580600-52598600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52580800-52598800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr3:52581000-52594600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52581000-52598400	Strong transcription	HUVEC	blood vessel
38	chr3:52581000-52601000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:52581400-52590200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52582000-52590000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:52582400-52591800	Weak transcription	A549	lung
42	chr3:52582400-52592000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:52582600-52596200	Strong transcription	GM12878-XiMat	blood
44	chr3:52583200-52590400	Strong transcription	Adipose Nuclei	Adipose
45	chr3:52583200-52594400	Strong transcription	Lung	lung
46	chr3:52583200-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:52583200-52600800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:52584200-52598600	Strong transcription	Fetal Lung	lung
49	chr3:52584400-52592200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52584400-52594600	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links