Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	CHRNA4
Previous Symbol	EBN, EBN1
Symbol Alias	BFNC
Approved Name	cholinergic receptor, nicotinic, alpha 4 (neuronal)
Previous Name	cholinergic receptor, nicotinic, alpha polypeptide 4
Name Alias	acetylcholine receptor, nicotinic, alpha 4 (neuronal)
Location	20q13.33
Position	chr20:63343223-63378401, -1
External Links	HGNC: 1958 Entrez Gene: 1137 Ensembl: ENSG00000101204 UCSC: uc002yes.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Shi, J., 2007	SNP: rs2273502, rs755203	rs1948 showed nominally significant transmission bias; haploview analyses showed nominally significant transmission bias of rs1948-rs7178270-rs1316971-rs11633223; no evidence of interaction among these 19 cholinergic genes by FITF analysis and FDR correction was found	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 36)

GO terms by PBA (count: 7)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0006816	calcium ion transport	biological process	ISS	14
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0006811	ion transport	biological process	NAS[8906617]	18
GO:0005886	plasma membrane	cellular component	ISS; TAS	360
GO:0016021	integral component of membrane	cellular component	NAS[8906617]	219
GO:0007268	synaptic transmission	biological process	NAS[7550350]; TAS	116
GO:0016020	membrane	cellular component	ISS	137

GO terms by database search (count: 29)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007165	signal transduction	biological process	IDA[8906617]	136
GO:0007271	synaptic transmission, cholinergic	biological process	ISS	14
GO:0001508	action potential	biological process	ISS	6
GO:0035640	exploration behavior	biological process	IEA	4
GO:0019233	sensory perception of pain	biological process	ISS	15
GO:0007626	locomotory behavior	biological process	IEA	23
GO:0005892	acetylcholine-gated channel complex	cellular component	IDA[8906617]	13
GO:0050890	cognition	biological process	IMP[14623738]	11
GO:0006979	response to oxidative stress	biological process	IMP[16332175]	11
GO:0030054	cell junction	cellular component	IEA	88
GO:0051899	membrane depolarization	biological process	ISS	9
GO:0001666	response to hypoxia	biological process	IDA[12189247]	24
GO:0006281	DNA repair	biological process	IMP[16332175]	16
GO:0015276	ligand-gated ion channel activity	molecular function	TAS[20438829]	7
GO:0009897	external side of plasma membrane	cellular component	ISS	21
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	IDA[8906617]; TAS[20438829]	13
GO:0030425	dendrite	cellular component	ISS	65
GO:0060080	regulation of inhibitory postsynaptic membrane potential	biological process	ISS	4
GO:0042113	B cell activation	biological process	ISS	3
GO:0050877	neurological system process	biological process	IMP[17613539]	4
GO:0035095	behavioral response to nicotine	biological process	IMP[17955458]	6
GO:0098655	cation transmembrane transport	biological process	IDA[8906617]; IEA; TAS[20438829]	16
GO:0043025	neuronal cell body	cellular component	ISS	50
GO:0042391	regulation of membrane potential	biological process	ISS	13
GO:0042166	acetylcholine binding	molecular function	IC[8906617]	9
GO:0014059	regulation of dopamine secretion	biological process	ISS	8
GO:0007585	respiratory gaseous exchange	biological process	IEA	3
GO:0015464	acetylcholine receptor activity	molecular function	IDA[8906617]	10
GO:0035094	response to nicotine	biological process	IDA[12189247]	10

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 3)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRNA4	CRELD2	YES	in vitro;yeast 2-hybrid	16238698
CHRNA4	VSNL1	NO	in vitro;in vivo;yeast 2-hybrid	12202488
CHRNA4	UBQLN1	NO	in vivo	16091357

Related other genetic factors

Gene related SNPs (count: 2)

Literature-origin SNPs (count: 2)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs755203	chr20:63362912 - 63362912(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2273502	chr20:63356470 - 63356470(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 0)

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 20	chr20:0-64444167	4 (0/3/1)
20p11-q13	chr20:17900000-64444167	1 (1/0/0)
20q13	chr20:43100000-64444167	2 (0/2/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with SZ from candidate gene intersection analysis (count: 2)

Reference	ID in SZGene	Result Category
16636791	741	Negative
18762859	741	Negative

Gene relationship with MDD

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Region: chr20:63343223..63378401 View in gBrowse