Genomic Context

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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 European 2 0.195 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 2 0.415 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Meta 57 0.416 N/A 1 0.019 404.6 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 5 0.420 N/A 1 5.3e-04 11.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 Meta 57 0.487 N/A 1 0.019 404.6 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 57 0.489 N/A 1 0.019 404.6 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 5 0.578 N/A 0 5.3e-04 11.0 PCs and sequencing center VEP HIGH N/A
NG00065 European 5 0.619 N/A 1 5.3e-04 11.0 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 Caribbean Hispanic 7 0.690 N/A 1 0.018 14.0 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 7 0.696 N/A 0 0.018 14.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 7 0.704 N/A 1 0.018 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 MOD-HIGH N/A
NG00065 European 52 0.709 N/A 1 0.016 329.4 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 52 0.840 N/A 1 0.016 329.4 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 European 52 0.842 N/A 1 0.016 329.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 2 0.866 N/A 0 1.4e-04 3.0 PCs and sequencing center LOF

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the PSEN2 gene.

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The PSEN2 gene contains 2,042 variants records (corresponding to 1,930 unique genomic positions).

The following variants, contained within ±100kb of PSEN2, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of PSEN2 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.

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of PSEN2 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of PSEN2, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of PSEN2 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 PSEN2 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 PSEN2 gene (chr1:227057885-227083806)

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:0042987 amyloid precursor protein catabolic process TAS
BP GO:0050435 beta-amyloid metabolic process IBA
BP GO:0006816 calcium ion transport IBA
BP GO:0048013 ephrin receptor signaling pathway TAS
BP GO:0035556 intracellular signal transduction IEA
BP GO:0006509 membrane protein ectodomain proteolysis IDA
BP GO:0031293 membrane protein intracellular domain proteolysis TAS
BP GO:0043066 negative regulation of apoptotic process IBA
BP GO:0007220 Notch receptor processing TAS
BP GO:0007219 Notch signaling pathway IEA,TAS
BP GO:0043065 positive regulation of apoptotic process TAS
BP GO:0043085 positive regulation of catalytic activity IDA
BP GO:0016485 protein processing IEA,IDA
BP GO:0006508 proteolysis IEA
BP GO:0001666 response to hypoxia IEA
CC GO:0016324 apical plasma membrane IBA
CC GO:0005938 cell cortex IBA
CC GO:0005813 centrosome IDA
CC GO:0005783 endoplasmic reticulum IDA,IEA
CC GO:0005789 endoplasmic reticulum membrane IEA
CC GO:0005794 Golgi apparatus IDA,IEA
CC GO:0000139 Golgi membrane IEA
CC GO:0016021 integral component of membrane IEA
CC GO:0005887 integral component of plasma membrane IDA
CC GO:0005622 intracellular IEA
CC GO:0000776 kinetochore IDA
CC GO:0016020 membrane IDA,IEA
CC GO:0043025 neuronal cell body IBA
CC GO:0005637 nuclear inner membrane IDA
CC GO:0048471 perinuclear region of cytoplasm IBA
CC GO:0005886 plasma membrane TAS
CC GO:0043234 protein complex IDA
CC GO:0030018 Z disc IBA
MF GO:0004190 aspartic-type endopeptidase activity IEA
MF GO:0004175 endopeptidase activity IBA
MF GO:0016787 hydrolase activity IEA
MF GO:0008233 peptidase activity IEA
MF GO:0005515 protein binding IPI

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
Alzheimer's disease hsa05010
Neurotrophin signaling pathway hsa04722
Notch signaling pathway hsa04330