Gene Page: CHRNA3

Summary ?
GeneID1136
SymbolCHRNA3
SynonymsLNCR2|NACHRA3|PAOD2
Descriptioncholinergic receptor nicotinic alpha 3 subunit
ReferenceMIM:118503|HGNC:HGNC:1957|Ensembl:ENSG00000080644|HPRD:07511|Vega:OTTHUMG00000143863
Gene typeprotein-coding
Map location15q24
Pascal p-value4.988E-9
eGeneCaudate basal ganglia
Nucleus accumbens basal ganglia
Putamen basal ganglia
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:PGC128Genome-wide Association StudyA multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 16 

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP IDChromosomePositionAllelePFunctionGeneUp/Down Distance
rs8042374chr1578908032AG1.865E-12intronicCHRNA3

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17130103chr188150541CHRNA311360.11trans
rs16823145chr1184397914CHRNA311360.04trans
rs6666913chr1237092144CHRNA311360.13trans
rs7596511chr2120010898CHRNA311360.01trans
rs2324466chr376100753CHRNA311360.15trans
rs17013713chr376105150CHRNA311360.05trans
rs17013722chr376107656CHRNA311360.15trans
rs17013724chr376107684CHRNA311360.15trans
rs16831155chr3173574763CHRNA311360.15trans
rs10212684chr4102822506CHRNA311360.1trans
rs9986296chr53199318CHRNA311360.12trans
rs348150chr873371619CHRNA311360.1trans
rs16938220chr873377940CHRNA311360.07trans
rs17233214chr1121367388CHRNA311360.13trans
rs2069410chr1256364644CHRNA311360.01trans
rs17834315chr1337991091CHRNA311360.06trans
rs10498433chr1452289530CHRNA311360.01trans
rs129007831578815523CHRNA3ENSG00000080644.111.393E-6098114gtex_brain_putamen_basal
rs125943911578816240CHRNA3ENSG00000080644.111.354E-6097397gtex_brain_putamen_basal
rs129109691578816980CHRNA3ENSG00000080644.111.323E-6096657gtex_brain_putamen_basal
rs129107261578817034CHRNA3ENSG00000080644.111.318E-6096603gtex_brain_putamen_basal
rs15045451578818471CHRNA3ENSG00000080644.111.259E-6095166gtex_brain_putamen_basal
rs9522151578819153CHRNA3ENSG00000080644.111.231E-6094484gtex_brain_putamen_basal
rs9522161578819202CHRNA3ENSG00000080644.111.229E-6094435gtex_brain_putamen_basal
rs129024931578819275CHRNA3ENSG00000080644.111.226E-6094362gtex_brain_putamen_basal
rs129031291578819606CHRNA3ENSG00000080644.111.214E-6094031gtex_brain_putamen_basal
rs116361311578821606CHRNA3ENSG00000080644.111.15E-6092031gtex_brain_putamen_basal
rs116326041578821914CHRNA3ENSG00000080644.111.141E-6091723gtex_brain_putamen_basal
rs129102891578822065CHRNA3ENSG00000080644.111.044E-6091572gtex_brain_putamen_basal
rs357731151578822189CHRNA3ENSG00000080644.112.036E-6091448gtex_brain_putamen_basal
rs129101001578822667CHRNA3ENSG00000080644.111.13E-6090970gtex_brain_putamen_basal
rs129154281578823368CHRNA3ENSG00000080644.111.124E-6090269gtex_brain_putamen_basal
rs129006121578823993CHRNA3ENSG00000080644.111.094E-6089644gtex_brain_putamen_basal
rs18475301578824031CHRNA3ENSG00000080644.111.119E-6089606gtex_brain_putamen_basal
rs15045461578824235CHRNA3ENSG00000080644.111.116E-6089402gtex_brain_putamen_basal
rs1450424031578824287CHRNA3ENSG00000080644.111.116E-6089350gtex_brain_putamen_basal
rs116303491578824608CHRNA3ENSG00000080644.111.115E-6089029gtex_brain_putamen_basal
rs129062841578825105CHRNA3ENSG00000080644.111.115E-6088532gtex_brain_putamen_basal
rs129074251578825149CHRNA3ENSG00000080644.111.115E-6088488gtex_brain_putamen_basal
rs129068461578825295CHRNA3ENSG00000080644.111.115E-6088342gtex_brain_putamen_basal
rs129071691578825498CHRNA3ENSG00000080644.111.115E-6088139gtex_brain_putamen_basal
rs129069511578825562CHRNA3ENSG00000080644.111.115E-6088075gtex_brain_putamen_basal
rs560074531578826239CHRNA3ENSG00000080644.111.115E-6087398gtex_brain_putamen_basal
rs174072571578826249CHRNA3ENSG00000080644.111.115E-6087388gtex_brain_putamen_basal
rs129169991578826912CHRNA3ENSG00000080644.111.115E-6086725gtex_brain_putamen_basal
rs129153661578831753CHRNA3ENSG00000080644.111.115E-6081884gtex_brain_putamen_basal
rs129156521578831928CHRNA3ENSG00000080644.111.115E-6081709gtex_brain_putamen_basal
rs129164831578832397CHRNA3ENSG00000080644.111.115E-6081240gtex_brain_putamen_basal
rs38135721578832588CHRNA3ENSG00000080644.111.115E-6081049gtex_brain_putamen_basal
rs38135711578832792CHRNA3ENSG00000080644.111.115E-6080845gtex_brain_putamen_basal
rs556906191578833612CHRNA3ENSG00000080644.111.28E-7080025gtex_brain_putamen_basal
rs48865711578833758CHRNA3ENSG00000080644.111.28E-7079879gtex_brain_putamen_basal
rs42430831578833830CHRNA3ENSG00000080644.111.324E-7079807gtex_brain_putamen_basal
rs22921171578834689CHRNA3ENSG00000080644.111.28E-7078948gtex_brain_putamen_basal
rs118582301578835552CHRNA3ENSG00000080644.111.28E-7078085gtex_brain_putamen_basal
rs80254291578836362CHRNA3ENSG00000080644.111.28E-7077275gtex_brain_putamen_basal
rs674378371578836631CHRNA3ENSG00000080644.111.308E-7077006gtex_brain_putamen_basal
rs767124481578836719CHRNA3ENSG00000080644.113.5E-7076918gtex_brain_putamen_basal
rs757543171578836721CHRNA3ENSG00000080644.113.424E-7076916gtex_brain_putamen_basal
rs784060671578836723CHRNA3ENSG00000080644.113.424E-7076914gtex_brain_putamen_basal
rs774342381578836726CHRNA3ENSG00000080644.113.532E-7076911gtex_brain_putamen_basal
rs283929481578836866CHRNA3ENSG00000080644.111.28E-7076771gtex_brain_putamen_basal
rs48865721578837452CHRNA3ENSG00000080644.111.28E-7076185gtex_brain_putamen_basal
rs48870621578837801CHRNA3ENSG00000080644.111.28E-7075836gtex_brain_putamen_basal
rs28695441578839400CHRNA3ENSG00000080644.116.625E-8074237gtex_brain_putamen_basal
rs48870631578839715CHRNA3ENSG00000080644.116.625E-8073922gtex_brain_putamen_basal
rs80531578841220CHRNA3ENSG00000080644.116.625E-8072417gtex_brain_putamen_basal
rs19799071578842239CHRNA3ENSG00000080644.116.625E-8071398gtex_brain_putamen_basal
rs19799061578842289CHRNA3ENSG00000080644.116.625E-8071348gtex_brain_putamen_basal
rs19799051578842374CHRNA3ENSG00000080644.116.625E-8071263gtex_brain_putamen_basal
rs3977601941578842835CHRNA3ENSG00000080644.111.638E-8070802gtex_brain_putamen_basal
rs48870641578842847CHRNA3ENSG00000080644.116.625E-8070790gtex_brain_putamen_basal
rs129079661578843051CHRNA3ENSG00000080644.111.346E-6070586gtex_brain_putamen_basal
rs15045481578843246CHRNA3ENSG00000080644.116.625E-8070391gtex_brain_putamen_basal
rs19799081578843564CHRNA3ENSG00000080644.116.625E-8070073gtex_brain_putamen_basal
rs8803951578844356CHRNA3ENSG00000080644.116.625E-8069281gtex_brain_putamen_basal
rs9057401578844386CHRNA3ENSG00000080644.116.625E-8069251gtex_brain_putamen_basal
rs71640301578844661CHRNA3ENSG00000080644.116.625E-8068976gtex_brain_putamen_basal
rs42758211578849541CHRNA3ENSG00000080644.112.143E-11064096gtex_brain_putamen_basal
rs71735121578849914CHRNA3ENSG00000080644.112.11E-11063723gtex_brain_putamen_basal
rs38297871578856266CHRNA3ENSG00000080644.112.409E-10057371gtex_brain_putamen_basal
rs8710581578858491CHRNA3ENSG00000080644.114.928E-8055146gtex_brain_putamen_basal
rs579454531578862845CHRNA3ENSG00000080644.112.018E-10050792gtex_brain_putamen_basal
rs5887651578865425CHRNA3ENSG00000080644.114.202E-8048212gtex_brain_putamen_basal
rs610124571578865694CHRNA3ENSG00000080644.112.106E-10047943gtex_brain_putamen_basal
rs64953061578865893CHRNA3ENSG00000080644.114.18E-8047744gtex_brain_putamen_basal
rs24560191578868489CHRNA3ENSG00000080644.116.291E-12045148gtex_brain_putamen_basal
rs6010791578869579CHRNA3ENSG00000080644.112.16E-7044058gtex_brain_putamen_basal
rs4959561578869930CHRNA3ENSG00000080644.111.084E-10043707gtex_brain_putamen_basal
rs4950901578870003CHRNA3ENSG00000080644.111.087E-10043634gtex_brain_putamen_basal
rs4718891578870235CHRNA3ENSG00000080644.111.09E-10043402gtex_brain_putamen_basal
rs6802441578871288CHRNA3ENSG00000080644.111.632E-7042349gtex_brain_putamen_basal
rs107099561578872834CHRNA3ENSG00000080644.111.763E-7040803gtex_brain_putamen_basal
rs6218491578872861CHRNA3ENSG00000080644.112.164E-7040776gtex_brain_putamen_basal
rs6927801578876505CHRNA3ENSG00000080644.116.649E-12037132gtex_brain_putamen_basal
rs116376351578877150CHRNA3ENSG00000080644.116.745E-12036487gtex_brain_putamen_basal
rs4811341578877563CHRNA3ENSG00000080644.114.276E-8036074gtex_brain_putamen_basal
rs58139271578878100CHRNA3ENSG00000080644.114.178E-8035537gtex_brain_putamen_basal
rs5550181578879242CHRNA3ENSG00000080644.112.913E-8034395gtex_brain_putamen_basal
rs6470411578880481CHRNA3ENSG00000080644.111.319E-8033156gtex_brain_putamen_basal
rs174082761578881618CHRNA3ENSG00000080644.112.146E-10032019gtex_brain_putamen_basal
rs5841351578883628CHRNA3ENSG00000080644.112.061E-12030009gtex_brain_putamen_basal
rs5147431578884227CHRNA3ENSG00000080644.111.722E-12029410gtex_brain_putamen_basal
rs6154701578885988CHRNA3ENSG00000080644.118.884E-12027649gtex_brain_putamen_basal
rs6606521578887832CHRNA3ENSG00000080644.111.718E-12025805gtex_brain_putamen_basal
rs4720541578887994CHRNA3ENSG00000080644.111.718E-12025643gtex_brain_putamen_basal
rs3980578511578889782CHRNA3ENSG00000080644.112.934E-8023855gtex_brain_putamen_basal
rs64953071578890321CHRNA3ENSG00000080644.112.934E-8023316gtex_brain_putamen_basal
rs129116021578891449CHRNA3ENSG00000080644.112.934E-8022188gtex_brain_putamen_basal
rs620103271578892784CHRNA3ENSG00000080644.116.853E-10020853gtex_brain_putamen_basal
rs129013001578892952CHRNA3ENSG00000080644.112.934E-8020685gtex_brain_putamen_basal
rs37430771578894896CHRNA3ENSG00000080644.111.735E-7018741gtex_brain_putamen_basal
rs620103281578894971CHRNA3ENSG00000080644.113.513E-10018666gtex_brain_putamen_basal
rs751047981578897865CHRNA3ENSG00000080644.117.203E-11015772gtex_brain_putamen_basal
rs71825831578899210CHRNA3ENSG00000080644.118.888E-12014427gtex_brain_putamen_basal
rs1117259591578899346CHRNA3ENSG00000080644.116.724E-11014291gtex_brain_putamen_basal
rs74955181578900574CHRNA3ENSG00000080644.113.595E-10013063gtex_brain_putamen_basal
rs1399789011578902026CHRNA3ENSG00000080644.119.923E-8011611gtex_brain_putamen_basal
rs1838224421578902775CHRNA3ENSG00000080644.112.634E-8010862gtex_brain_putamen_basal
rs1902598911578902906CHRNA3ENSG00000080644.111.287E-7010731gtex_brain_putamen_basal
rs774038741578903165CHRNA3ENSG00000080644.111.081E-7010472gtex_brain_putamen_basal
rs96461871578906128CHRNA3ENSG00000080644.111.882E-1007509gtex_brain_putamen_basal
rs28695461578907345CHRNA3ENSG00000080644.112.265E-1106292gtex_brain_putamen_basal
rs37430751578909452CHRNA3ENSG00000080644.118.892E-904185gtex_brain_putamen_basal
rs37430741578909480CHRNA3ENSG00000080644.117.993E-1004157gtex_brain_putamen_basal
rs37430731578909539CHRNA3ENSG00000080644.111.716E-904098gtex_brain_putamen_basal
rs20678081578911780CHRNA3ENSG00000080644.116.746E-1101857gtex_brain_putamen_basal
rs18783991578912003CHRNA3ENSG00000080644.112.291E-801634gtex_brain_putamen_basal
rs2015766271578912201CHRNA3ENSG00000080644.113.817E-701436gtex_brain_putamen_basal
rs43666831578912203CHRNA3ENSG00000080644.113.078E-701434gtex_brain_putamen_basal
rs3864195581578912203CHRNA3ENSG00000080644.111.478E-701434gtex_brain_putamen_basal
rs43520171578912204CHRNA3ENSG00000080644.111.343E-701433gtex_brain_putamen_basal
rs80251881578912278CHRNA3ENSG00000080644.112.431E-701359gtex_brain_putamen_basal
rs80234621578914734CHRNA3ENSG00000080644.112.037E-120-1097gtex_brain_putamen_basal
rs48870701578916187CHRNA3ENSG00000080644.113.896E-110-2550gtex_brain_putamen_basal
rs29041301578916622CHRNA3ENSG00000080644.111.453E-130-2985gtex_brain_putamen_basal
rs19481578917399CHRNA3ENSG00000080644.113E-120-3762gtex_brain_putamen_basal
rs620103321578918762CHRNA3ENSG00000080644.111.342E-130-5125gtex_brain_putamen_basal
rs71782701578921077CHRNA3ENSG00000080644.117.694E-90-7440gtex_brain_putamen_basal
rs9507761578926018CHRNA3ENSG00000080644.118.286E-100-12381gtex_brain_putamen_basal
rs796092841578928411CHRNA3ENSG00000080644.113.242E-70-14774gtex_brain_putamen_basal
rs577282261578929350CHRNA3ENSG00000080644.111.726E-60-15713gtex_brain_putamen_basal
rs360458691578929498CHRNA3ENSG00000080644.111.726E-60-15861gtex_brain_putamen_basal
rs116378901578935419CHRNA3ENSG00000080644.111.797E-70-21782gtex_brain_putamen_basal
rs116332231578935476CHRNA3ENSG00000080644.111.797E-70-21839gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0030594neurotransmitter receptor activityIEANeurotransmitter (GO term level: 5)-
GO:0015464acetylcholine receptor activityIDANeurotransmitter (GO term level: 6)8906617 
GO:0004889nicotinic acetylcholine-activated cation-selective channel activityIDA8906617 
GO:0004889nicotinic acetylcholine-activated cation-selective channel activityIEA-
GO:0005216ion channel activityIEA-
GO:0005230extracellular ligand-gated ion channel activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0060084synaptic transmission involved in micturitionIEAneuron, Synap (GO term level: 8)-
GO:0060084synaptic transmission involved in micturitionIMPneuron, Synap (GO term level: 8)11450844 
GO:0060079regulation of excitatory postsynaptic membrane potentialIEAneuron, Synap (GO term level: 10)-
GO:0060079regulation of excitatory postsynaptic membrane potentialISSneuron, Synap (GO term level: 10)-
GO:0007271synaptic transmission, cholinergicIEAneuron, Cholinergic, Synap, Neurotransmitter (GO term level: 7)-
GO:0007271synaptic transmission, cholinergicISSneuron, Cholinergic, Synap, Neurotransmitter (GO term level: 7)-
GO:0014056regulation of acetylcholine secretionIEANeurotransmitter (GO term level: 10)-
GO:0014056regulation of acetylcholine secretionISSNeurotransmitter (GO term level: 10)-
GO:0048814regulation of dendrite morphogenesisIEAdendrite (GO term level: 13)-
GO:0048814regulation of dendrite morphogenesisISSdendrite (GO term level: 13)-
GO:0007399nervous system developmentIMPneurite (GO term level: 5)11450844 
GO:0007165signal transductionIDA8906617 
GO:0007626locomotory behaviorIEA-
GO:0007626locomotory behaviorISS-
GO:0006811ion transportIEA-
GO:0006811ion transportNAS8906617 
GO:0006940regulation of smooth muscle contractionIEA-
GO:0006940regulation of smooth muscle contractionISS-
GO:0007171activation of transmembrane receptor protein tyrosine kinase activityIEA-
GO:0007171activation of transmembrane receptor protein tyrosine kinase activityISS-
GO:0042391regulation of membrane potentialIEA-
GO:0042391regulation of membrane potentialISS-
GO:0035095behavioral response to nicotineIEA-
GO:0035095behavioral response to nicotineIMP18227835 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005892nicotinic acetylcholine-gated receptor-channel complexIDANeurotransmitter (GO term level: 9)8906617 
GO:0005892nicotinic acetylcholine-gated receptor-channel complexIEANeurotransmitter (GO term level: 9)-
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0016021integral to membraneIEA-
GO:0016021integral to membraneNAS8906617 
GO:0005886plasma membraneIEA-
GO:0030054cell junctionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 272195All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 137110All SZGR 2.0 genes in this pathway
REACTOME ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 1613All SZGR 2.0 genes in this pathway
REACTOME HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 1312All SZGR 2.0 genes in this pathway
REACTOME PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 1210All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184125All SZGR 2.0 genes in this pathway
GRABARCZYK BCL11B TARGETS DN 5735All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP 162116All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP 1821933All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN 172112All SZGR 2.0 genes in this pathway
KANG GIST WITH PDGFRA UP 5027All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL UP 3922All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP 8961All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY NO BLOOD UP 222139All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED 536296All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590403All SZGR 2.0 genes in this pathway