Gene Page: SMARCD3

Summary ?
GeneID6604
SymbolSMARCD3
SynonymsBAF60C|CRACD3|Rsc6p
DescriptionSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3
ReferenceMIM:601737|HGNC:HGNC:11108|Ensembl:ENSG00000082014|HPRD:03440|Vega:OTTHUMG00000157431
Gene typeprotein-coding
Map location7q35-q36
Pascal p-value0.08
Sherlock p-value0.375
Fetal beta0.268
DMG1 (# studies)
eGeneMyers' cis & trans
SupportChromatin Remodeling Genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg000929677151000789SMARCD32.45E-10-0.0186.18E-7DMG:Jaffe_2016
cg084876967150945928SMARCD32.86E-8-0.0138.87E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7158406chr1440156482SMARCD366040.16trans
rs2781346chr1440163474SMARCD366040.14trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005102receptor bindingIPINeurotransmitter (GO term level: 4)14701856 
GO:0003713transcription coactivator activityTAS8804307 
GO:0008134transcription factor bindingIPI14701856 
GO:0030528transcription regulator activityIDA14701856 
GO:0035257nuclear hormone receptor bindingIPI14701856 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0003007heart morphogenesisIEA-
GO:0006357regulation of transcription from RNA polymerase II promoterTAS8804307 
GO:0016568chromatin modificationIEA-
GO:0042692muscle cell differentiationIEA-
GO:0043393regulation of protein bindingIEA-
GO:0045893positive regulation of transcription, DNA-dependentIDA14701856 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIDA14701856 
GO:0005654nucleoplasmTAS8804307 
GO:0016514SWI/SNF complexNAS14701856 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID LKB1 PATHWAY 4737All SZGR 2.0 genes in this pathway
PID TAP63 PATHWAY 5440All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 3627All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION 10472All SZGR 2.0 genes in this pathway
REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION 2417All SZGR 2.0 genes in this pathway
REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION 2416All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 2316All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY 352181All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478302All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 168115All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN CLOCK 5340All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 7253All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN 309191All SZGR 2.0 genes in this pathway
TIMOFEEVA GROWTH STRESS VIA STAT1 DN 1612All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP 158103All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP 341197All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP 10075All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL 326213All SZGR 2.0 genes in this pathway
KOMMAGANI TP63 GAMMA TARGETS 97All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP 309199All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN 411249All SZGR 2.0 genes in this pathway
ROSS AML WITH PML RARA FUSION 7762All SZGR 2.0 genes in this pathway
MARIADASON REGULATED BY HISTONE ACETYLATION UP 8349All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP 317208All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP 461298All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4 196124All SZGR 2.0 genes in this pathway
CROONQUIST STROMAL STIMULATION UP 6042All SZGR 2.0 genes in this pathway
CROONQUIST NRAS VS STROMAL STIMULATION DN 9965All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP 166105All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756494All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL DN 308187All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway