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	BCL9
Approved Name	B-cell CLL/lymphoma 9
Location	1q21
Position	chr1:147541412-147626216, 1
External Links	HGNC: 1008 Entrez Gene: 607 Ensembl: ENSG00000116128 UCSC: uc031uul.1
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Li, J.,2011(b)	SNP: rs10494251, rs1240083, rs1541187, rs2236570, rs3766512, rs671056, rs672607, rs688325, rs9326555, rs946903	These findings indicate that common variations in the BCL9 gene confer risk of schizophrenia and may also be associated with bipolar disorder and major depressive disorder in the Chinese Han population.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 11)

GO terms by PBA (count: 0)

GO terms by database search (count: 11)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005794	Golgi apparatus	cellular component	IEA	60
GO:0005801	cis-Golgi network	cellular component	IDA[23386608]	3
GO:0035914	skeletal muscle cell differentiation	biological process	IEA	4
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IEA	91
GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	biological process	IMP[19328798]	1
GO:0014908	myotube differentiation involved in skeletal muscle regeneration	biological process	IEA	1
GO:0005654	nucleoplasm	cellular component	TAS	163
GO:0008013	beta-catenin binding	molecular function	IEA	14
GO:0035019	somatic stem cell maintenance	biological process	IEA	6
GO:0060070	canonical Wnt signaling pathway	biological process	IEA	9
GO:0005515	protein binding	molecular function	IPI[11955446]	563

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
BCL9	PYGO1	NO	in vitro;in vivo;yeast 2-hybrid	11955446 , 14612447
BCL9	PYGO2	NO	in vitro;in vivo;yeast 2-hybrid	11955446 , 14612447
BCL9	CTNNB1	NO	in vivo;yeast 2-hybrid	15294866

Related other genetic factors

Gene related SNPs (count: 70)

Literature-origin SNPs (count: 10)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs672607	chr1:147581540 - 147581540(1)	intron_variant	1(1/0/0)
rs946903	chr1:147625465 - 147625465(1)	3_prime_UTR_variant; downstream_gene_variant	1(0/1/0)
rs1541187	chr1:147579693 - 147579693(1)	intron_variant	1(0/1/0)
rs2236570	chr1:147622086 - 147622086(1)	intron_variant	1(0/1/0)
rs688325	chr1:147605490 - 147605490(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs10494251	chr1:147552120 - 147552120(1)	intron_variant	1(0/1/0)
rs671056	chr1:147546461 - 147546461(1)	intron_variant	1(0/1/0)
rs9326555	chr1:147550532 - 147550532(1)	intron_variant	1(0/1/0)
rs3766512	chr1:147625834 - 147625834(1)	3_prime_UTR_variant; downstream_gene_variant	1(0/1/0)
rs1240083	chr8:89051573 - 89051573(1)		1(0/1/0)

LD-proxies (count: 60)

rs_ID	Location	Functional Annotation
rs666106	chr1:147582273 - 147582273(1)	intron_variant
rs614502	chr1:147585422 - 147585422(1)	intron_variant
rs644105	chr1:147587606 - 147587606(1)	intron_variant
rs637784	chr1:147588546 - 147588546(1)	intron_variant
rs672619	chr1:147586773 - 147586773(1)	intron_variant
rs645388	chr1:147587326 - 147587326(1)	intron_variant
rs12122799	chr1:147610227 - 147610227(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs7526407	chr1:147598816 - 147598816(1)	intron_variant; upstream_gene_variant
rs12132534	chr1:147627185 - 147627185(1)	downstream_gene_variant
rs2353525	chr1:147597199 - 147597199(1)	intron_variant; upstream_gene_variant
rs17160476	chr1:147621873 - 147621873(1)	intron_variant
rs6675828	chr1:147615167 - 147615167(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7512513	chr1:147614705 - 147614705(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs1390507	chr1:147588435 - 147588435(1)	intron_variant
rs6695965	chr1:147588292 - 147588292(1)	intron_variant
rs10900382	chr1:147586995 - 147586995(1)	intron_variant
rs10900379	chr1:147583057 - 147583057(1)	intron_variant
rs10465881	chr1:147595529 - 147595529(1)	intron_variant; upstream_gene_variant
rs10793693	chr1:147592510 - 147592510(1)	intron_variant
rs2132441	chr1:147590782 - 147590782(1)	intron_variant
rs11240081	chr1:147578197 - 147578197(1)	intron_variant
rs11240089	chr1:147588715 - 147588715(1)	intron_variant
rs1546161	chr1:147558681 - 147558681(1)	intron_variant
rs1027423	chr1:147546759 - 147546759(1)	intron_variant
rs1027424	chr1:147546591 - 147546591(1)	intron_variant
rs17160408	chr1:147548867 - 147548867(1)	intron_variant
rs17361839	chr1:147627887 - 147627887(1)	downstream_gene_variant
rs12076319	chr1:147547011 - 147547011(1)	intron_variant
rs12037951	chr1:147631053 - 147631053(1)	downstream_gene_variant; stop_lost
rs10494250	chr1:147552273 - 147552273(1)	intron_variant
rs677977	chr1:147611945 - 147611945(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs12081028	chr1:147550923 - 147550923(1)	intron_variant
rs597577	chr1:147617106 - 147617106(1)	downstream_gene_variant; intron_variant
rs613089	chr1:147609390 - 147609390(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs17160461	chr1:147578078 - 147578078(1)	intron_variant
rs583583	chr1:147611315 - 147611315(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs6657449	chr1:147543772 - 147543772(1)	intron_variant
rs11240077	chr1:147544678 - 147544678(1)	intron_variant
rs10494252	chr1:147545166 - 147545166(1)	intron_variant
rs17160420	chr1:147552868 - 147552868(1)	intron_variant
rs634309	chr1:147551494 - 147551494(1)	intron_variant
rs17160433	chr1:147556878 - 147556878(1)	intron_variant
rs1390510	chr1:147559545 - 147559545(1)	intron_variant
rs17160434	chr1:147560802 - 147560802(1)	intron_variant
rs4950461	chr1:147561794 - 147561794(1)	intron_variant
rs17160421	chr1:147553022 - 147553022(1)	intron_variant
rs17160422	chr1:147553100 - 147553100(1)	intron_variant
rs17160424	chr1:147553923 - 147553923(1)	intron_variant
rs17160431	chr1:147556092 - 147556092(1)	intron_variant
rs594132	chr1:147542066 - 147542066(1)	intron_variant
rs627219	chr1:147601562 - 147601562(1)	intron_variant; non_coding_transcript_variant
rs17160413	chr1:147549648 - 147549648(1)	intron_variant
rs10793690	chr1:147563798 - 147563798(1)	intron_variant
rs17160437	chr1:147565690 - 147565690(1)	intron_variant
rs594206	chr1:147548685 - 147548685(1)	intron_variant
rs17160448	chr1:147573064 - 147573064(1)	intron_variant
rs649001	chr1:147594483 - 147594483(1)	intron_variant
rs6667707	chr1:147627080 - 147627080(1)	downstream_gene_variant
rs2297961	chr1:147630356 - 147630356(1)	3_prime_UTR_variant; downstream_gene_variant
rs867270	chr1:147624993 - 147624993(1)	3_prime_UTR_variant; downstream_gene_variant

Gene related CNVs (count: 1)

ID	Location	Size	Band	Type	Inheritance
CNV_Abdul Noor[2014]_1	chr1:144943150-146293282 (NCBI Build 36/hg18)	1	1q21.1	duplication

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
1p13.2-1q21.3	chr1:111200000-155100000	1 (1/0/0)
1p32.1-q31.1	chr1:58500000-190800000	1 (0/1/0)
Chr 1	chr1:0-248956422	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: 1)

Reference	Description	Result Category
21383261	These findings indicate that common variations in the BCL9 gene confer risk of schizophrenia and may also be associated with bipolar disorder and major depressive disorder in the Chinese Han population.	Positive

Overlap with SZ from candidate gene intersection analysis (count: 0)

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 1)

Reference	Description	Category in MDD
21383261	These findings indicate that common variations in the BCL9 gene confer risk of schizophrenia and may also be associated with bipolar disorder and major depressive disorder in the Chinese Han population.	Positive

Overlap with MDD from candidate gene intersection analysis (count: 0)

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Region: chr1:147541412..147626216 View in gBrowse