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.

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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 Meta 91 0.028 N/A 1 9.8e-03 212.5 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 85 0.042 N/A 1 9.7e-03 202.5 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 91 0.054 N/A 1 9.8e-03 212.5 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 85 0.080 N/A 1 9.7e-03 202.5 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 8 0.157 N/A 0 0.013 10.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 8 0.177 N/A 0 0.013 10.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 1 0.189 N/A 0 4.8e-05 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 1 0.189 N/A 0 4.8e-05 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 1 0.192 N/A 0 4.8e-05 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 European 1 0.192 N/A 0 4.8e-05 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 8 0.195 N/A 0 0.013 10.0 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 91 0.303 N/A 0 9.8e-03 212.5 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 1 0.344 N/A 0 4.8e-05 1.0 PCs and sequencing center LOF
NG00065 European 1 0.344 N/A 0 4.8e-05 1.0 PCs and sequencing center VEP HIGH
NG00065 European 85 0.370 N/A 0 9.7e-03 202.5 PCs and sequencing center VEP MOD-HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the EPHB4 gene.

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The EPHB4 gene contains 2,332 variants records (corresponding to 2,175 unique genomic positions).

The following variants, contained within ±100kb of EPHB4, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of EPHB4 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 EPHB4 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of EPHB4, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of EPHB4 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 EPHB4 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 EPHB4 gene (chr7:100400187-100425121)

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:0001525 angiogenesis IEA,ISS
BP GO:0007155 cell adhesion IDA
BP GO:0002042 cell migration involved in sprouting angiogenesis IDA
BP GO:0048013 ephrin receptor signaling pathway IDA,IEA,TAS
BP GO:0003007 heart morphogenesis ISS
BP GO:0007275 multicellular organism development IEA
BP GO:0018108 peptidyl-tyrosine phosphorylation IEA
BP GO:0016310 phosphorylation IEA
BP GO:0046777 protein autophosphorylation IDA
BP GO:0006468 protein phosphorylation IEA
BP GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway IEA
CC GO:0005829 cytosol TAS
CC GO:0070062 extracellular exosome IDA
CC GO:0005576 extracellular region TAS
CC GO:0016021 integral component of membrane IEA
CC GO:0005887 integral component of plasma membrane IDA,IEA
CC GO:0016020 membrane IEA
CC GO:0005886 plasma membrane IEA,TAS
MF GO:0005524 ATP binding IEA
MF GO:0005003 ephrin receptor activity IEA,IDA
MF GO:0016301 kinase activity IEA
MF GO:0000166 nucleotide binding IEA
MF GO:0005515 protein binding IPI
MF GO:0004672 protein kinase activity IEA
MF GO:0004713 protein tyrosine kinase activity IEA
MF GO:0016740 transferase activity IEA
MF GO:0004714 transmembrane receptor protein tyrosine kinase activity IEA,IDA

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
Axon guidance hsa04360