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PTK2B - ENSG00000120899

protein tyrosine kinase 2 beta

Also known as: CAKB, PYK2, RAFTK, PTK, CADTK

Location: chr8:27,168,999-27,316,903

Gene Type: protein coding

More information
NCBI Gene
2185
HUGO
HGNC:9612
Ensembl
ENSG00000120899
VEGA
OTTHUMG00000102082
OMIM
601212
UniProtKB
Q14289

Genomic Context

The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.

To add tracks, use the provided link to switch to the full genome browser view.

Gene-based Trait Associations

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ADSP WES: Alzheimer's Disease ADSP

Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.

Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.

See NIAGADS Accession NG00065 for more information.

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Accession Population N SNPs p-value Sign. Level rho CMAF CMAC Covariates Variant Filter Caveats
NG00065 Caribbean Hispanic 10 0.299 N/A 1 0.027 21.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 10 0.315 N/A 1 0.027 21.7 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 10 0.323 N/A 1 0.027 21.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 1 0.373 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Caribbean Hispanic 1 0.373 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Caribbean Hispanic 1 0.382 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH
NG00065 Caribbean Hispanic 1 0.382 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Caribbean Hispanic 1 0.410 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.410 N/A 0 1.3e-03 1.0 PCs and sequencing center LOF
NG00065 European 5 0.503 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 European 5 0.503 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 Meta 6 0.534 N/A 0 6.9e-04 15.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 European 113 0.687 N/A 0 0.032 666.4 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 118 0.696 N/A 0 0.032 688.1 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 5 0.720 N/A 0 6.7e-04 14.0 PCs and sequencing center LOF N/A
NG00065 European 5 0.720 N/A 0 6.7e-04 14.0 PCs and sequencing center VEP HIGH N/A
NG00065 European 5 0.747 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 European 5 0.747 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 Meta 6 0.750 N/A 0 6.9e-04 15.0 PCs and sequencing center VEP HIGH N/A
NG00065 Meta 6 0.778 N/A 0 6.9e-04 15.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 Meta 118 0.792 N/A 1 0.032 688.1 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 113 0.918 N/A 0 0.032 666.4 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 Meta 118 0.928 N/A 0 0.032 688.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 113 0.928 N/A 0 0.032 666.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the PTK2B gene.

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The PTK2B gene contains 9,069 variants records (corresponding to 8,736 unique genomic positions).

The following variants, contained within ±100kb of PTK2B, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of PTK2B that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

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Relative Position Variant ADSP? Allele p-Value Track Accession
in gene C 7.4e-14 IGAP 2013: Stages 1 and 2 NG00036
in gene T 4.2e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 5.2e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 6.9e-13 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 6.9e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 6.9e-13 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene A 7.7e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 9.2e-12 IGAP 2013: Stages 1 and 2 NG00036
in gene C 1.5e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream G 6.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 3.3e-9 IGAP 2013: Stage 1 NG00036
in gene T 3.7e-9 IGAP (2013): ADGC Subset NG00053
in gene A 4.8e-9 IGAP (2013): ADGC Subset NG00053
in gene A 5.3e-9 IGAP 2013: Stage 1 NG00036
in gene G 8.8e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.0e-8 IGAP (2013): ADGC Subset NG00053
in gene A 1.1e-8 IGAP (2013): ADGC Subset NG00053
in gene A 1.1e-8 IGAP 2013: Stage 1 NG00036
in gene G 1.2e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.4e-8 IGAP 2013: Stage 1 NG00036
downstream C 1.6e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.7e-8 IGAP (2013): ADGC Subset NG00053
downstream T 1.7e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene C 2.2e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene T 2.5e-8 Transethnic LOAD: All Samples NG00056
in gene T 3.5e-8 Transethnic LOAD: All Samples NG00056
downstream T 3.9e-8 IGAP 2013: Stages 1 and 2 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of PTK2B that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of PTK2B, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of PTK2B that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of PTK2B that are associated with a trait in the NHGRI GWAS Catalog.

Functional Genomics

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Explore all functional genomics annotations within the region of the PTK2B gene (chr8:27168999-27316903)

Transcription Factor Binding Site Overlap in Gene Promoter Region (ENCODE ChIP-SEQ)

ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.

Functional Annotation

Gene Ontology

Functional annotations were obtained from UniProt-GOA gene association files.

Click on a term accession number to view term details at the Gene Ontology Consortium.

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Ontology GO Accession Term Evidence Code
BP GO:0007015 actin filament organization IEA
BP GO:0090630 activation of GTPase activity IEA
BP GO:0042976 activation of Janus kinase activity IEA,IMP
BP GO:0002250 adaptive immune response IEA
BP GO:0001525 angiogenesis IBA,IEA
BP GO:0006915 apoptotic process TAS
BP GO:0043534 blood vessel endothelial cell migration IEA
BP GO:0045453 bone resorption IEA,ISS
BP GO:0007155 cell adhesion IEA
BP GO:0030154 cell differentiation IEA
BP GO:0007166 cell surface receptor signaling pathway IMP
BP GO:0006968 cellular defense response IEA,ISS
BP GO:0071498 cellular response to fluid shear stress IEA
BP GO:0071300 cellular response to retinoic acid IMP
BP GO:0070098 chemokine-mediated signaling pathway IEA,ISS
BP GO:0007173 epidermal growth factor receptor signaling pathway IBA,IEA
BP GO:0048041 focal adhesion assembly IEA
BP GO:0014009 glial cell proliferation IEA
BP GO:0002376 immune system process IEA
BP GO:0045087 innate immune response IBA
BP GO:0007229 integrin-mediated signaling pathway IMP
BP GO:0035235 ionotropic glutamate receptor signaling pathway IEA,ISS
BP GO:0060292 long term synaptic depression IEA
BP GO:0060291 long-term synaptic potentiation ISS,IEA
BP GO:0000165 MAPK cascade IEA
BP GO:0002315 marginal zone B cell differentiation IEA,ISS
BP GO:0043066 negative regulation of apoptotic process IEA,IMP
BP GO:0030502 negative regulation of bone mineralization ISS,IEA
BP GO:0008285 negative regulation of cell proliferation IMP
BP GO:0010656 negative regulation of muscle cell apoptotic process IEA
BP GO:0045638 negative regulation of myeloid cell differentiation IMP
BP GO:0043524 negative regulation of neuron apoptotic process IEA,ISS
BP GO:0030279 negative regulation of ossification IEA
BP GO:0043267 negative regulation of potassium ion transport IDA
BP GO:0031175 neuron projection development IEA
BP GO:0001556 oocyte maturation IEA
BP GO:0038083 peptidyl-tyrosine autophosphorylation IEA,ISS,IDA
BP GO:0018108 peptidyl-tyrosine phosphorylation IEA,IDA
BP GO:0016310 phosphorylation IEA
BP GO:0030838 positive regulation of actin filament polymerization IMP
BP GO:0045766 positive regulation of angiogenesis IEA
BP GO:2000538 positive regulation of B cell chemotaxis ISS,IEA
BP GO:0030307 positive regulation of cell growth IEA
BP GO:0001954 positive regulation of cell-matrix adhesion IMP
BP GO:0030335 positive regulation of cell migration IEA,IMP
BP GO:0008284 positive regulation of cell proliferation TAS,IMP,IEA
BP GO:0032270 positive regulation of cellular protein metabolic process IEA
BP GO:0007204 positive regulation of cytosolic calcium ion concentration IEA
BP GO:2000573 positive regulation of DNA biosynthetic process IEA
BP GO:0010595 positive regulation of endothelial cell migration IEA,IDA
BP GO:0070374 positive regulation of ERK1 and ERK2 cascade IMP
BP GO:2000463 positive regulation of excitatory postsynaptic potential IEA,ISS
BP GO:0046330 positive regulation of JNK cascade IMP
BP GO:0043507 positive regulation of JUN kinase activity IEA
BP GO:0010976 positive regulation of neuron projection development IMP
BP GO:0045429 positive regulation of nitric oxide biosynthetic process IEA
BP GO:0051000 positive regulation of nitric-oxide synthase activity IEA
BP GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation IDA
BP GO:0043552 positive regulation of phosphatidylinositol 3-kinase activity IEA,ISS
BP GO:0045860 positive regulation of protein kinase activity IEA,IMP
BP GO:2000060 positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process IEA
BP GO:2000379 positive regulation of reactive oxygen species metabolic process IEA
BP GO:0051968 positive regulation of synaptic transmission, glutamatergic IEA,ISS
BP GO:0045727 positive regulation of translation IEA
BP GO:0046777 protein autophosphorylation TAS
BP GO:0006461 protein complex assembly TAS
BP GO:0006468 protein phosphorylation IEA,TAS
BP GO:2000249 regulation of actin cytoskeleton reorganization ISS,IEA
BP GO:0045765 regulation of angiogenesis IEA
BP GO:0030500 regulation of bone mineralization IEA
BP GO:0050848 regulation of calcium-mediated signaling IEA
BP GO:0030155 regulation of cell adhesion IEA,IMP
BP GO:0030334 regulation of cell migration IEA
BP GO:0042127 regulation of cell proliferation IEA
BP GO:0008360 regulation of cell shape IEA,IMP
BP GO:0030826 regulation of cGMP biosynthetic process IEA
BP GO:0010752 regulation of cGMP-mediated signaling IEA
BP GO:2000114 regulation of establishment of cell polarity IEA,ISS
BP GO:0032960 regulation of inositol trisphosphate biosynthetic process ISS,IEA
BP GO:0002688 regulation of leukocyte chemotaxis IEA
BP GO:0010758 regulation of macrophage chemotaxis IEA,ISS
BP GO:0045428 regulation of nitric oxide biosynthetic process IEA
BP GO:2000310 regulation of N-methyl-D-aspartate selective glutamate receptor activity IEA,ISS
BP GO:2000058 regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process IDA
BP GO:0051279 regulation of release of sequestered calcium ion into cytosol IEA,ISS
BP GO:0051592 response to calcium ion IEA
BP GO:0051591 response to cAMP IEA
BP GO:0042220 response to cocaine IEA
BP GO:0042493 response to drug IEA
BP GO:0045471 response to ethanol IEA
BP GO:0009749 response to glucose IEA
BP GO:0009725 response to hormone IEA
BP GO:0042542 response to hydrogen peroxide IEA
BP GO:0001666 response to hypoxia IEA
BP GO:0035902 response to immobilization stress IEA
BP GO:0010226 response to lithium ion IEA
BP GO:0009612 response to mechanical stimulus IEA
BP GO:0010243 response to organonitrogen compound IEA
BP GO:0006970 response to osmotic stress IEA
BP GO:0000302 response to reactive oxygen species IEA
BP GO:0006950 response to stress TAS
BP GO:0007172 signal complex assembly TAS,IEA
BP GO:0007165 signal transduction TAS,IEA
BP GO:0002040 sprouting angiogenesis IEA,ISS
BP GO:0043149 stress fiber assembly IEA
BP GO:0033209 tumor necrosis factor-mediated signaling pathway IMP
BP GO:0048010 vascular endothelial growth factor receptor signaling pathway TAS,IEA,IMP
CC GO:0097440 apical dendrite ISS,IEA
CC GO:0030424 axon IEA
CC GO:0044297 cell body ISS,IEA
CC GO:0005938 cell cortex IEA
CC GO:0030054 cell junction IEA
CC GO:0042995 cell projection IEA
CC GO:0005737 cytoplasm TAS,IEA
CC GO:0005856 cytoskeleton IEA
CC GO:0005829 cytosol TAS
CC GO:0030425 dendrite ISS,IEA
CC GO:0043197 dendritic spine IEA
CC GO:0031234 extrinsic component of cytoplasmic side of plasma membrane IBA,IEA
CC GO:0005925 focal adhesion IDA,IEA
CC GO:0030426 growth cone ISS,IEA
CC GO:0030027 lamellipodium IDA,IEA
CC GO:0016020 membrane IEA
CC GO:0045121 membrane raft IEA
CC GO:0043025 neuronal cell body IEA,ISS
CC GO:0017146 NMDA selective glutamate receptor complex IEA,ISS
CC GO:0005634 nucleus IDA,IEA
CC GO:0048471 perinuclear region of cytoplasm IDA,IEA
CC GO:0005886 plasma membrane IEA
CC GO:0014069 postsynaptic density ISS,IEA
MF GO:0043423 3-phosphoinositide-dependent protein kinase binding IEA
MF GO:0005524 ATP binding IEA
MF GO:0004683 calmodulin-dependent protein kinase activity ISS,IEA
MF GO:0019899 enzyme binding IEA
MF GO:0016301 kinase activity IEA
MF GO:0004972 NMDA glutamate receptor activity ISS,IEA
MF GO:0004715 non-membrane spanning protein tyrosine kinase activity IEA,TAS,IDA
MF GO:0000166 nucleotide binding IEA
MF GO:0005515 protein binding IPI
MF GO:0032403 protein complex binding IEA
MF GO:0004672 protein kinase activity IEA
MF GO:0004713 protein tyrosine kinase activity IDA,IEA,TAS
MF GO:0005102 receptor binding IBA
MF GO:0004871 signal transducer activity IEA,NAS
MF GO:0016740 transferase activity IEA
MF GO:0031625 ubiquitin protein ligase binding IEA

KEGG Pathways

Click on a pathway accession number to view term details at KEGG.

Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.

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Pathway KEGG Accession Graph
Calcium signaling pathway hsa04020
Chemokine signaling pathway hsa04062
GnRH signaling pathway hsa04912
Hepatitis B hsa05161
Leukocyte transendothelial migration hsa04670
Natural killer cell mediated cytotoxicity hsa04650
Phospholipase D signaling pathway hsa04072