Gene Report

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Basic Info

Approved Symbol	CHRNB4
Approved Name	cholinergic receptor, nicotinic, beta 4 (neuronal)
Previous Name	cholinergic receptor, nicotinic, beta polypeptide 4
Name Alias	acetylcholine receptor, nicotinic, beta 4 (neuronal)
Location	15q24
Position	chr15:78624119-78727754, -1
External Links	HGNC: 1964 Entrez Gene: 1143 Ensembl: ENSG00000117971 UCSC: uc002bed.1
No. of Studies	2 (Positive: 1; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Shi, J., 2007	SNP: rs11633223, rs1316971, rs1948, rs7178270 Haplotype: rs1948 - rs7178270 - rs1316971 - rs11633223(G-C-G-G)	no evidence of interaction among these 19 cholinergic genes was found by Allelic Association, Haploview Tests, FITF analysis and FDR correction	Negative	Comment on Study
Jackson, K. J., 2013	SNP: rs17487223	Variants in the 15q25 gene cluster are associated with risk for schizophrenia/bipolar illness, negative symptoms of schizophrenia, and influence CHRNA5 expression in the brain and peripheral blood mononuclear cells.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 23)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016021	integral component of membrane	cellular component	NAS[8906617]	219
GO:0006812	cation transport	biological process	TAS[11742001]	8
GO:0005887	integral component of plasma membrane	cellular component	IC[11742001]	158
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0006811	ion transport	biological process	TAS[8906617]	18

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0034220	ion transmembrane transport	biological process	TAS[20438829]	50
GO:0060084	synaptic transmission involved in micturition	biological process	IMP[11450844]	3
GO:0001508	action potential	biological process	IEA	6
GO:0098655	cation transmembrane transport	biological process	IEA; TAS[11742001]	16
GO:0005892	acetylcholine-gated channel complex	cellular component	IDA[8906617]; TAS[11742001]	13
GO:0007165	signal transduction	biological process	IDA[8906617]	136
GO:0007626	locomotory behavior	biological process	IEA	23
GO:0030054	cell junction	cellular component	IEA	88
GO:0046928	regulation of neurotransmitter secretion	biological process	NAS[11742001]	7
GO:0007271	synaptic transmission, cholinergic	biological process	TAS[1330682]	14
GO:0015276	ligand-gated ion channel activity	molecular function	TAS[20438829]	7
GO:0035095	behavioral response to nicotine	biological process	IEA	6
GO:0015464	acetylcholine receptor activity	molecular function	IDA[8906617]	10
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	TAS[11742001]	13
GO:0006939	smooth muscle contraction	biological process	IEA	7
GO:0006940	regulation of smooth muscle contraction	biological process	IEA	5

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRNB4	CHRNA4	YES	in vitro	8906617
CHRNB4	UBQLN1	NO	in vivo	16091357

Related other genetic factors

Gene related SNPs (count: 13)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs1948	chr15:78625057 - 78625057(1)	3_prime_UTR_variant; downstream_gene_variant; synonymous_variant; upstream_gene_variant	1(1/0/0)
rs6495309	chr15:78622903 - 78622903(1)	downstream_gene_variant; upstream_gene_variant	1(0/1/0)
rs11633223	chr15:78643134 - 78643134(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs1316971	chr15:78638168 - 78638168(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs7178270	chr15:78628735 - 78628735(1)	downstream_gene_variant; intron_variant	1(0/1/0)
rs17487223	chr15:78631645 - 78631645(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)

rs_ID	Location	Functional Annotation
rs950776	chr15:78633676 - 78633676(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11637890	chr15:78643077 - 78643077(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs11636753	chr15:78636604 - 78636604(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1878399	chr15:78619661 - 78619661(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs11636605	chr15:78636536 - 78636536(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11072768	chr15:78637136 - 78637136(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12441998	chr15:78637030 - 78637030(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant

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)
15q25-26	chr15:78000000-101991189	1 (1/0/0)
15q24.1-25.2	chr15:72400000-84700000	1 (0/1/0)
Chr 15	chr15:0-101991189	2 (0/2/0)

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

Gene relationship with SZ

Reference	Description	Result Category
23196875	Variants in the 15q25 gene cluster are associated with risk for schizophrenia/bipolar illness, negative symptoms of schizophrenia, and influence CHRNA5 expression in the brain and peripheral blood mononuclear cells.	Positive

Gene relationship with MDD

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Region: chr15:78624119..78727754 View in gBrowse