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	CHRNA9
Symbol Alias	NACHRA9
Approved Name	cholinergic receptor, nicotinic, alpha 9 (neuronal)
Previous Name	cholinergic receptor, nicotinic, alpha polypeptide 9
Name Alias	acetylcholine receptor, nicotinic, alpha 9 (neuronal)
Location	4p14
Position	chr4:40335329-40355217, 1
External Links	HGNC: 14079 Entrez Gene: 55584 Ensembl: ENSG00000174343 UCSC: uc003gva.2
No. of Studies	2 (Positive: 0; Negative: 2; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Yosifova, A.,2011	SNP: rs4447895	No significant association of this gene was observed in BD.	Negative	Comment on Study
Shi, J., 2007	SNP: rs10805117, rs4264869, rs4861065, rs6819483, rs6823439	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

Gene functional annotation

Gene related GO terms (count: 13)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0005887	integral component of plasma membrane	cellular component	IDA[25282151]	158
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0005262	calcium channel activity	molecular function	IEA	9

GO terms by database search (count: 8)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0050910	detection of mechanical stimulus involved in sensory perception of sound	biological process	IEA	2
GO:0070588	calcium ion transmembrane transport	biological process	IEA	24
GO:0005892	acetylcholine-gated channel complex	cellular component	IDA[25282151]	13
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	IEA	13
GO:0042472	inner ear morphogenesis	biological process	IEA	8
GO:0022848	acetylcholine-gated cation channel activity	molecular function	IDA[25282151]	2
GO:0007204	positive regulation of cytosolic calcium ion concentration	biological process	IGI[18420419]	21
GO:0030054	cell junction	cellular component	IEA	88

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 0)

Related other genetic factors

Gene related SNPs (count: 30)

Literature-origin SNPs (count: 6)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs4264869	chr4:40353109 - 40353109(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs6823439	chr4:40334583 - 40334583(1)	downstream_gene_variant; upstream_gene_variant	1(0/1/0)
rs6819483	chr4:40347325 - 40347325(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs4861065	chr4:40342378 - 40342378(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs4447895	chr4:40395236 - 40395236(1)		1(0/1/0)
rs10805117	chr4:40330821 - 40330821(1)	downstream_gene_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 24)

rs_ID	Location	Functional Annotation
rs4861298	chr4:40332894 - 40332894(1)	downstream_gene_variant; upstream_gene_variant
rs7673930	chr4:40331504 - 40331504(1)	downstream_gene_variant; upstream_gene_variant
rs7679386	chr4:40331850 - 40331850(1)	downstream_gene_variant; upstream_gene_variant
rs6816902	chr4:40333646 - 40333646(1)	downstream_gene_variant; upstream_gene_variant
rs10022491	chr4:40335891 - 40335891(1)	synonymous_variant; upstream_gene_variant
rs6819385	chr4:40337557 - 40337557(1)	intron_variant; non_coding_transcript_variant
rs7669882	chr4:40348634 - 40348634(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs6828585	chr4:40336313 - 40336313(1)	intron_variant; upstream_gene_variant
rs4469116	chr4:40335231 - 40335231(1)	downstream_gene_variant; upstream_gene_variant
rs4469115	chr4:40334910 - 40334910(1)	downstream_gene_variant; upstream_gene_variant
rs6838680	chr4:40332835 - 40332835(1)	downstream_gene_variant; upstream_gene_variant
rs10015231	chr4:40335549 - 40335549(1)	intron_variant; upstream_gene_variant
rs13138234	chr4:40330698 - 40330698(1)	downstream_gene_variant; upstream_gene_variant
rs10938311	chr4:40331307 - 40331307(1)	downstream_gene_variant; upstream_gene_variant
rs4861307	chr4:40343222 - 40343222(1)	intron_variant; non_coding_transcript_variant
rs4547831	chr4:40345058 - 40345058(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs12509596	chr4:40341020 - 40341020(1)	intron_variant; non_coding_transcript_variant
rs4861306	chr4:40343001 - 40343001(1)	intron_variant; non_coding_transcript_variant
rs10001509	chr4:40349860 - 40349860(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs10938433	chr4:40355309 - 40355309(1)	downstream_gene_variant
rs4568270	chr4:40345218 - 40345218(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10029872	chr4:40348746 - 40348746(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs10006948	chr4:40356898 - 40356898(1)	downstream_gene_variant
rs10004757	chr4:40358113 - 40358113(1)	downstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 4	chr4:0-190214555	3 (0/3/0)
4p14-p15	chr4:11300000-41200000	1 (0/1/0)
4p14-p13	chr4:35800000-44600000	1 (0/0/1)
4p	chr4:0-50000000	1 (0/1/0)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr4:40335329..40355217 View in gBrowse