Gene Page: JARID2

Summary ?
GeneID3720
SymbolJARID2
SynonymsJMJ
Descriptionjumonji and AT-rich interaction domain containing 2
ReferenceMIM:601594|HGNC:HGNC:6196|Ensembl:ENSG00000008083|HPRD:03355|Vega:OTTHUMG00000014293
Gene typeprotein-coding
Map location6p24-p23
Pascal p-value0.519
Sherlock p-value0.273
TADA p-value0.023
Fetal beta1.085
eGeneMyers' cis & trans
SupportCompositeSet
Ascano FMRP targets
Chromatin Remodeling Genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies2Link to SZGene
GSMA_IGenome scan meta-analysisPsr: 0.0159 
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

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
JARID2chr615501497GANM_001267040
NM_004973		p.597G>S
p.769G>S		missense
missense		SchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs16829545chr2151977407JARID237209.49E-6trans
rs7584986chr2184111432JARID237200.07trans
rs3118341chr925185518JARID237200.1trans
rs2393316chr1059333070JARID237200.02trans
rs16955618chr1529937543JARID237205.528E-8trans
rs1041786chr2122617710JARID237200.01trans

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
SCN8A0.970.95
GRIN2A0.960.80
KCNMA10.950.90
ARHGAP260.950.88
ATP2B20.940.94
DLGAP20.940.88
PLCB10.940.90
GABRB20.940.89
KCNH10.930.77
BSN0.930.91
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
BCL7C-0.46-0.56
AC006276.2-0.44-0.47
C9orf46-0.42-0.46
RPL35-0.41-0.54
RPLP1-0.41-0.49
RPL23A-0.41-0.47
RAB13-0.40-0.53
GTF3C6-0.40-0.39
EFEMP2-0.40-0.39
RPL36-0.40-0.49

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003677DNA bindingIEA-
GO:0005515protein bindingIEA-
GO:0016564transcription repressor activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007417central nervous system developmentTASBrain (GO term level: 6)8894700 
GO:0000122negative regulation of transcription from RNA polymerase II promoterIEA-
GO:0001889liver developmentIEA-
GO:0006350transcriptionIEA-
GO:0008285negative regulation of cell proliferationIEA-
GO:0007275multicellular organismal developmentIEA-
GO:0048536spleen developmentIEA-
GO:0048538thymus developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005622intracellularIEA-
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
DAVICIONI MOLECULAR ARMS VS ERMS UP 332228All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN 508354All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION DN 234147All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS F UP 185119All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP 1037673All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514330All SZGR 2.0 genes in this pathway
BENPORATH ES 1 379235All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290172All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH NOS TARGETS 179105All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
MORI PRE BI LYMPHOCYTE DN 7749All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE UP 5335All SZGR 2.0 genes in this pathway
TENEDINI MEGAKARYOCYTE MARKERS 6648All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH REARRANGEMENTS DN 4826All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV SCC DN 12386All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN 215132All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN 318220All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC UP 202115All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G6 153112All SZGR 2.0 genes in this pathway
SAFFORD T LYMPHOCYTE ANERGY 8754All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 528324All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4 307185All SZGR 2.0 genes in this pathway
ZHENG BOUND BY FOXP3 491310All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
ZHENG FOXP3 TARGETS IN THYMUS UP 196137All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409268All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP 430288All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP 439257All SZGR 2.0 genes in this pathway
MIKKELSEN DEDIFFERENTIATED STATE UP 85All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP 207143All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 227149All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF 516308All SZGR 2.0 genes in this pathway