Variant report

Variant	rs4234644
Chromosome Location	chr3:51695865-51695866
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11719995	0.89[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.84[CEU][hapmap]
rs13090011	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821829	0.86[CEU][hapmap]
rs4067	0.84[CEU][hapmap]
rs4317086	0.83[EUR][1000 genomes]
rs4355273	0.86[CEU][hapmap]
rs4468965	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4494918	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687721	1.00[CEU][hapmap]
rs4687770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4687771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6775666	0.84[CEU][hapmap]
rs6787312	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9841077	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864443	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864693	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866430	0.89[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4234644	TEX264	cis	Esophagus Muscularis	GTEx
rs4234644	TEX264	cis	Nerve Tibial	GTEx
rs4234644	TEX264	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51680000-51696000	Weak transcription	A549	lung
2	chr3:51680800-51702800	Weak transcription	K562	blood
3	chr3:51681000-51697000	Weak transcription	Stomach Mucosa	stomach
4	chr3:51681600-51703200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:51682200-51704400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:51682400-51696200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:51682400-51696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:51682400-51696600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:51682600-51702800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:51687800-51698000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:51687800-51698600	Strong transcription	Primary T cells from cord blood	blood
12	chr3:51687800-51699400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:51687800-51700000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:51687800-51700200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:51688000-51697400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:51688000-51698200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:51688000-51701000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:51688000-51701800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:51688000-51702200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:51688000-51702400	Strong transcription	Fetal Stomach	stomach
21	chr3:51688200-51700000	Strong transcription	Placenta	Placenta
22	chr3:51688400-51698400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:51688600-51697800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:51688600-51698000	Strong transcription	Thymus	Thymus
25	chr3:51688600-51698400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:51688600-51698400	Strong transcription	Adipose Nuclei	Adipose
27	chr3:51688600-51700000	Strong transcription	Fetal Intestine Large	intestine
28	chr3:51688600-51700200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:51688600-51701200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:51688800-51698000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:51688800-51700200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:51688800-51700600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:51689000-51696600	Weak transcription	Right Ventricle	heart
34	chr3:51689000-51697600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:51689000-51697600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:51689000-51699000	Strong transcription	Brain Hippocampus Middle	brain
37	chr3:51689000-51699600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:51689000-51700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:51689200-51698800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:51689200-51699600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:51689200-51700200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:51689400-51697800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:51689400-51697800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:51689400-51698000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:51689400-51698400	Strong transcription	Dnd41	blood
46	chr3:51689400-51698600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:51689400-51700000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:51689600-51697400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr3:51689600-51697800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:51689600-51698400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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