Gene Report

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Basic Info

Approved Symbol	ARNTL2
Symbol Alias	BMAL2, MOP9, CLIF, PASD9, bHLHe6
Approved Name	aryl hydrocarbon receptor nuclear translocator-like 2
Location	12p12.2-p11.2
Position	chr12:27332854-27425289, 1
External Links	HGNC: 18984 Entrez Gene: 56938 Ensembl: ENSG00000029153 UCSC: uc001rhu.2
No. of Studies	3 (Positive: 1; Negative: 2; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 3)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Soria, V.,2010	SNP: rs10506018, rs10842905, rs11048994, rs11048995, rs11610949, rs2970844, rs35878285, rs3751222, rs4964060	Significant associations of ARNTL2 gene were found in BPD patients.	Positive	Comment on Study
Mansour, H. A.,2009		Gene-based tests:X<sup>2</sup>=4.067, P-value = 0.559 in recessive model, X<sup>2</sup>=4.068, P-value = 0.591 in dominant model, X<sup>2</sup>=3.171, P-value = 0.699 in additive model in BPI. No significant association was observed using neither single SNP-based analyses nor gene-based tests in BPI.	Negative	Comment on Study
Byrne, E. M., 2014		P-value=0.36. Gene-based tests show no significant association between this gene and BD.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 18)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0004871	signal transducer activity	molecular function	IEA	32
GO:0005634	nucleus	cellular component	IDA; NAS[11018023]	283
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	IDA[12055078]; NAS[11018023]	66

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0006366	transcription from RNA polymerase II promoter	biological process	IDA[15147242]	31
GO:0000982	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity	molecular function	IDA[15147242]	3
GO:0042753	positive regulation of circadian rhythm	biological process	ISS	3
GO:0005737	cytoplasm	cellular component	IEA	322
GO:0070888	E-box binding	molecular function	IDA[12738229]	7
GO:0007165	signal transduction	biological process	IEA	136
GO:0005730	nucleolus	cellular component	IDA	28
GO:0046983	protein dimerization activity	molecular function	IEA	19
GO:0006357	regulation of transcription from RNA polymerase II promoter	biological process	IDA[12055078]	21
GO:0009649	entrainment of circadian clock	biological process	NAS[11018023]	2
GO:0005667	transcription factor complex	cellular component	IEA	18
GO:0007623	circadian rhythm	biological process	IDA[10864977]	40
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[15147242]	91
GO:0006355	regulation of transcription, DNA-templated	biological process	NAS[11018023]	62
GO:0045893	positive regulation of transcription, DNA-templated	biological process	IDA[12738229]	58

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
ARNTL2	CLOCK	YES	in vitro;in vivo	10864977 , 11018023
ARNTL2	EPAS1	NO	in vitro;yeast 2-hybrid	11018023

Related other genetic factors

Gene related SNPs (count: 19)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs11048995	chr12:27378502 - 27378502(1)	downstream_gene_variant; intron_variant	1(1/0/0)
rs4964060	chr12:27380434 - 27380434(1)	downstream_gene_variant; intron_variant	1(1/0/0)
rs10506018	chr12:27342924 - 27342924(1)	intron_variant	1(1/0/0)
rs10842905	chr12:27329970 - 27329970(1)	downstream_gene_variant; upstream_gene_variant	1(1/0/0)
rs11610949	chr12:27334535 - 27334535(1)	intron_variant	1(1/0/0)
rs3751222	chr12:27387456 - 27387456(1)	downstream_gene_variant; intron_variant	1(0/1/0)
rs35878285	chr12:27403456 - 27403456(1)	intron_variant; missense_variant; non_coding_transcript_variant	1(1/0/0)
rs2970844	chr12:27351264 - 27351264(1)	intron_variant	1(1/0/0)
rs11048994	chr12:27377845 - 27377845(1)	downstream_gene_variant; intron_variant	1(1/0/0)

rs_ID	Location	Functional Annotation
rs17497857	chr12:27346668 - 27346668(1)	intron_variant
rs17497683	chr12:27343673 - 27343673(1)	intron_variant
rs17413765	chr12:27362443 - 27362443(1)	intron_variant
rs17413695	chr12:27361298 - 27361298(1)	intron_variant
rs17497502	chr12:27336479 - 27336479(1)	intron_variant
rs17413842	chr12:27369990 - 27369990(1)	intron_variant; non_coding_transcript_variant
rs12319133	chr12:27396149 - 27396149(1)	intron_variant; non_coding_transcript_variant
rs12299407	chr12:27396250 - 27396250(1)	intron_variant; non_coding_transcript_variant
rs11048998	chr12:27393444 - 27393444(1)	intron_variant; non_coding_transcript_variant
rs922270	chr12:27352018 - 27352018(1)	intron_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 12	chr12:0-133275309	3 (0/3/0)
12p11	chr12:26300000-35500000	1 (0/1/0)

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

Gene relationship with SZ

Reference	Description	Result Category
19839995	Gene-based tests:X<sup>2</sup>=6.36, P-value = 0.196 in dominant model in SZ/SZA, X<sup>2</sup>=4.7, P-value = 0.434 in recessive model in SZ/SZA, X<sup>2</sup>=3.236, P-value = 0.678 in additive model in SZ/SZA.No association was observed using neither single SNP-based analyses nor gene-based tests in SZ/SZA.	Negative
24687905	P-value=0.42. Gene-based tests show no significant association between this gene and SZ.	Negative

Reference	ID in SZGene	Result Category
19839995	876	Negative

Gene relationship with MDD

Reference	Description	Category in MDD
20072116	Significant associations of ARNTL2 gene were found in MDD patients.	Positive
24687905	P-value=0.95. Gene-based tests show no significant association between this gene and MDD.	Negative

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Region: chr12:27332854..27425289 View in gBrowse