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 Caribbean Hispanic 5 0.019 N/A 1 0.014 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 MOD-HIGH N/A
NG00065 Meta 37 0.022 N/A 1 0.023 503.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 5 0.025 N/A 1 0.014 11.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 5 0.026 N/A 1 0.014 11.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 37 0.067 N/A 1 0.023 503.7 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 European 34 0.074 N/A 1 0.022 466.2 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 37 0.143 N/A 1 0.023 503.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 3 0.284 N/A 1 2.4e-04 5.0 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 European 34 0.288 N/A 1 0.022 466.2 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 1 0.319 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 0.330 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 Meta 4 0.336 N/A 1 2.8e-04 6.0 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 0.347 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP HIGH
NG00065 European 3 0.355 N/A 0 2.4e-04 5.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Meta 4 0.440 N/A 1 2.8e-04 6.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 34 0.456 N/A 1 0.022 466.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 4 0.774 N/A 1 2.8e-04 6.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.815 N/A 0 1.9e-04 4.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 2 0.878 N/A 0 1.9e-04 4.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 European 2 0.898 N/A 0 1.9e-04 4.0 PCs and sequencing center LOF
NG00065 European 3 0.905 N/A 0 2.4e-04 5.0 PCs and sequencing center VEP HIGH

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the PSEN1 gene.

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The PSEN1 gene contains 4,975 variants records (corresponding to 4,779 unique genomic positions).

The following variants, contained within ±100kb of PSEN1, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of PSEN1 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 PSEN1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of PSEN1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of PSEN1 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 PSEN1 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 PSEN1 gene (chr14:73603126-73690399)

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:0000186 activation of MAPKK activity IEA
BP GO:0042987 amyloid precursor protein catabolic process IEA,TAS
BP GO:0042982 amyloid precursor protein metabolic process IDA
BP GO:0006915 apoptotic process IEA
BP GO:0000045 autophagosome assembly IEA
BP GO:0006914 autophagy IEA
BP GO:0034205 beta-amyloid formation IMP,IEA
BP GO:0050435 beta-amyloid metabolic process IEA
BP GO:0001568 blood vessel development IEA
BP GO:0007420 brain development IEA
BP GO:0048854 brain morphogenesis IEA
BP GO:0021870 Cajal-Retzius cell differentiation IEA
BP GO:0070588 calcium ion transmembrane transport IEA
BP GO:0060070 canonical Wnt signaling pathway IBA
BP GO:0007155 cell adhesion IEA
BP GO:0001708 cell fate specification IEA
BP GO:0006874 cellular calcium ion homeostasis IEA
BP GO:0044267 cellular protein metabolic process IEA
BP GO:0006974 cellular response to DNA damage stimulus IEA
BP GO:0021795 cerebral cortex cell migration IEA
BP GO:0021987 cerebral cortex development IEA
BP GO:0015871 choline transport IEA
BP GO:0021904 dorsal/ventral neural tube patterning IEA
BP GO:0030326 embryonic limb morphogenesis IEA
BP GO:0032469 endoplasmic reticulum calcium ion homeostasis IEA,IDA,IGI
BP GO:0050673 epithelial cell proliferation IEA
BP GO:0030900 forebrain development IEA
BP GO:0007507 heart development IEA
BP GO:0001947 heart looping IEA
BP GO:0002244 hematopoietic progenitor cell differentiation IEA
BP GO:0035556 intracellular signal transduction IEA
BP GO:0007611 learning or memory IEA
BP GO:0015813 L-glutamate transport IEA
BP GO:0040011 locomotion IEA
BP GO:0006509 membrane protein ectodomain proteolysis IEA,IDA
BP GO:0007613 memory IEA
BP GO:0006839 mitochondrial transport IEA
BP GO:0043011 myeloid dendritic cell differentiation IEA
BP GO:0002573 myeloid leukocyte differentiation IEA
BP GO:0043066 negative regulation of apoptotic process IEA,IDA
BP GO:2001234 negative regulation of apoptotic signaling pathway IEA
BP GO:0050771 negative regulation of axonogenesis IEA
BP GO:0007175 negative regulation of epidermal growth factor-activated receptor activity IEA
BP GO:0043524 negative regulation of neuron apoptotic process IEA
BP GO:0006469 negative regulation of protein kinase activity IEA
BP GO:0001933 negative regulation of protein phosphorylation IEA
BP GO:2000059 negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process IEA
BP GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA
BP GO:0051444 negative regulation of ubiquitin-protein transferase activity IEA
BP GO:0003407 neural retina development IEA
BP GO:0022008 neurogenesis IEA
BP GO:0051402 neuron apoptotic process IEA
BP GO:0048666 neuron development IEA
BP GO:0030182 neuron differentiation IEA
BP GO:0001764 neuron migration IEA
BP GO:0043312 neutrophil degranulation TAS
BP GO:0007220 Notch receptor processing IEA,TAS
BP GO:0007219 Notch signaling pathway IEA
BP GO:0043065 positive regulation of apoptotic process IEA
BP GO:0043085 positive regulation of catalytic activity IDA
BP GO:0050820 positive regulation of coagulation IEA
BP GO:0060999 positive regulation of dendritic spine development IMP
BP GO:0043406 positive regulation of MAP kinase activity IEA
BP GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
BP GO:0045860 positive regulation of protein kinase activity IEA
BP GO:0001934 positive regulation of protein phosphorylation IEA
BP GO:0001921 positive regulation of receptor recycling IEA
BP GO:0045893 positive regulation of transcription, DNA-templated IMP
BP GO:0009791 post-embryonic development IEA
BP GO:0006486 protein glycosylation IEA
BP GO:0051604 protein maturation IEA
BP GO:0016485 protein processing IDA,IEA
BP GO:0015031 protein transport IEA
BP GO:0006508 proteolysis IEA
BP GO:0060828 regulation of canonical Wnt signaling pathway IEA,ISS
BP GO:0007176 regulation of epidermal growth factor-activated receptor activity IEA
BP GO:0042325 regulation of phosphorylation IDA
BP GO:0043393 regulation of protein binding IEA
BP GO:0060075 regulation of resting membrane potential IEA
BP GO:0048167 regulation of synaptic plasticity IEA
BP GO:0051966 regulation of synaptic transmission, glutamatergic IEA
BP GO:0006979 response to oxidative stress IEA
BP GO:0035282 segmentation IEA
BP GO:0016337 single organismal cell-cell adhesion IMP
BP GO:0048705 skeletal system morphogenesis IEA
BP GO:0043589 skin morphogenesis IEA
BP GO:0051563 smooth endoplasmic reticulum calcium ion homeostasis IEA,IBA
BP GO:0001756 somitogenesis IEA
BP GO:0016080 synaptic vesicle targeting IEA
BP GO:0002286 T cell activation involved in immune response IEA
BP GO:0050852 T cell receptor signaling pathway IEA
BP GO:0048538 thymus development IEA
CC GO:0016235 aggresome IDA
CC GO:0030424 axon IEA
CC GO:0035577 azurophil granule membrane TAS
CC GO:0005938 cell cortex IEA
CC GO:0030054 cell junction IDA
CC GO:0009986 cell surface IEA
CC GO:0005813 centrosome IDA
CC GO:0035253 ciliary rootlet IEA
CC GO:0005737 cytoplasm IEA
CC GO:0031410 cytoplasmic vesicle IEA
CC GO:0030425 dendrite IEA
CC GO:0043198 dendritic shaft IEA
CC GO:0005783 endoplasmic reticulum IDA,IEA
CC GO:0005789 endoplasmic reticulum membrane IEA
CC GO:0070765 gamma-secretase complex IDA
CC GO:0005794 Golgi apparatus IDA,IEA
CC GO:0000139 Golgi membrane IEA
CC GO:0030426 growth cone IEA
CC GO:0016021 integral component of membrane TAS,IDA,IEA
CC GO:0005887 integral component of plasma membrane IDA
CC GO:0005622 intracellular IEA
CC GO:0000776 kinetochore IDA
CC GO:0005765 lysosomal membrane IEA
CC GO:0016020 membrane TAS,IDA,IEA
CC GO:0043227 membrane-bounded organelle IEA
CC GO:0045121 membrane raft IEA,IDA
CC GO:0005743 mitochondrial inner membrane IEA
CC GO:0005739 mitochondrion IDA,IEA
CC GO:0031594 neuromuscular junction IEA
CC GO:0043025 neuronal cell body IEA
CC GO:0043005 neuron projection IEA
CC GO:0031965 nuclear membrane IDA
CC GO:0005640 nuclear outer membrane IDA
CC GO:0005634 nucleus IEA,IDA
CC GO:0005886 plasma membrane IEA,IDA,TAS
CC GO:0098793 presynapse IEA
CC GO:0043234 protein complex IEA
CC GO:0005791 rough endoplasmic reticulum IDA
CC GO:0005790 smooth endoplasmic reticulum IDA
MF GO:0042500 aspartic endopeptidase activity, intramembrane cleaving IDA
MF GO:0004190 aspartic-type endopeptidase activity IEA
MF GO:0008013 beta-catenin binding IPI
MF GO:0045296 cadherin binding IEA,IBA
MF GO:0005262 calcium channel activity IMP
MF GO:0004175 endopeptidase activity IDA,IEA
MF GO:0016787 hydrolase activity IEA
MF GO:0030165 PDZ domain binding IPI
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
Wnt signaling pathway hsa04310