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	CHAT
Approved Name	choline O-acetyltransferase
Previous Name	choline acetyltransferase
Location	10q11.2
Position	chr10:49609095-49665104, 1
External Links	HGNC: 1912 Entrez Gene: 1103 Ensembl: ENSG00000070748 UCSC: uc001jhz.2
No. of Studies	1 (Positive: 0; Negative: 1; 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: rs10082479, rs1917810, rs1917813, rs3793791, rs6537546, rs7094248, rs885834	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: 21)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0005634	nucleus	cellular component	TAS[10861222]	283

GO terms by database search (count: 19)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007529	establishment of synaptic specificity at neuromuscular junction	biological process	IEA	1
GO:0005829	cytosol	cellular component	TAS	223
GO:0007628	adult walking behavior	biological process	IEA	9
GO:0043179	rhythmic excitation	biological process	IEA	1
GO:0006644	phospholipid metabolic process	biological process	TAS	18
GO:0007274	neuromuscular synaptic transmission	biological process	IEA	5
GO:0042136	neurotransmitter biosynthetic process	biological process	IEA	10
GO:0006656	phosphatidylcholine biosynthetic process	biological process	TAS	2
GO:0046474	glycerophospholipid biosynthetic process	biological process	TAS	5
GO:0007269	neurotransmitter secretion	biological process	TAS	15
GO:0007517	muscle organ development	biological process	IEA	11
GO:0030424	axon	cellular component	IEA	39
GO:0004102	choline O-acetyltransferase activity	molecular function	IEA	1
GO:0005737	cytoplasm	cellular component	TAS[10861222]	322
GO:0016358	dendrite development	biological process	IEA	8
GO:0043025	neuronal cell body	cellular component	IEA	50
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0007622	rhythmic behavior	biological process	IEA	2
GO:0005739	mitochondrion	cellular component	IEA	75

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa00564	Glycerophospholipid metabolism	7

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 8)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHAT	PRKCB	NO	in vitro	15381704
CHAT	CAMK2A	YES	in vitro;in vivo	12486117 , 10861222
CHAT	PRKCA	NO	in vitro;in vivo	12486117 , 10861222 , 15381704
CHAT	PRKCE	YES	in vitro	15381704
CHAT	PRKCG	NO	in vitro	15381704
CHAT	CAMK2G	NO	in vitro;in vivo	12486117
CHAT	NEDD9	NO	in vivo	10692442
CHAT	PRKCD	NO	in vitro	15381704

Related other genetic factors

Gene related SNPs (count: 29)

Literature-origin SNPs (count: 7)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs885834	chr10:49607466 - 49607466(1)	upstream_gene_variant	1(0/1/0)
rs6537546	chr10:49655997 - 49655997(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs1917813	chr10:49649789 - 49649789(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs7094248	chr10:49647322 - 49647322(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs3793791	chr10:49633658 - 49633658(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs10082479	chr10:49621173 - 49621173(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs1917810	chr10:49662025 - 49662025(1)	intron_variant; NMD_transcript_variant	1(0/1/0)

LD-proxies (count: 22)

rs_ID	Location	Functional Annotation
rs7903496	chr10:49651583 - 49651583(1)	intron_variant; NMD_transcript_variant
rs8178992	chr10:49655101 - 49655101(1)	3_prime_UTR_variant; missense_variant; NMD_transcript_variant; synonymous_variant
rs1917811	chr10:49649931 - 49649931(1)	intron_variant; NMD_transcript_variant
rs10776585	chr10:49650140 - 49650140(1)	intron_variant; NMD_transcript_variant
rs10776586	chr10:49650300 - 49650300(1)	intron_variant; NMD_transcript_variant
rs6537544	chr10:49651199 - 49651199(1)	intron_variant; NMD_transcript_variant
rs6537545	chr10:49651203 - 49651203(1)	intron_variant; NMD_transcript_variant
rs7900310	chr10:49651438 - 49651438(1)	intron_variant; NMD_transcript_variant
rs10857528	chr10:49664200 - 49664200(1)	intron_variant; NMD_transcript_variant
rs7076926	chr10:49655519 - 49655519(1)	intron_variant; NMD_transcript_variant
rs12358284	chr10:49661116 - 49661116(1)	intron_variant; NMD_transcript_variant
rs4838541	chr10:49644137 - 49644137(1)	intron_variant; NMD_transcript_variant
rs6537547	chr10:49659398 - 49659398(1)	intron_variant; NMD_transcript_variant
rs4838549	chr10:49656646 - 49656646(1)	intron_variant; NMD_transcript_variant
rs12264845	chr10:49655037 - 49655037(1)	intron_variant; NMD_transcript_variant
rs4838547	chr10:49654358 - 49654358(1)	intron_variant; NMD_transcript_variant
rs11101202	chr10:49664356 - 49664356(1)	intron_variant; NMD_transcript_variant
rs3793798	chr10:49663420 - 49663420(1)	intron_variant; NMD_transcript_variant
rs10857527	chr10:49662473 - 49662473(1)	intron_variant; NMD_transcript_variant
rs10857526	chr10:49661537 - 49661537(1)	intron_variant; NMD_transcript_variant
rs10857529	chr10:49667456 - 49667456(1)	downstream_gene_variant
rs2103082	chr10:49665982 - 49665982(1)	downstream_gene_variant

Gene related CNVs (count: 1)

ID	Location	Size	Band	Type	Inheritance
CNV_McQuillin[2011]_17	chr10:50334496-50490772 (NCBI Build 36 (hg18))	156277

Gene related other variants (count: 0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
10p11.21-q22.1	chr10:34200000-73100000	1 (1/0/0)
Chr 10	chr10:0-133797422	3 (0/2/1)
10q11.21-q22.1	chr10:41600000-73100000	1 (0/0/1)
10q11-q21	chr10:39800000-68800000	1 (0/1/0)

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: 1)

Reference	ID in SZGene	Result Category
17503482	520	Positive

Gene relationship with MDD

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Region: chr10:49609095..49665104 View in gBrowse