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 12 0.141 N/A 0 0.059 47.0 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 Caribbean Hispanic 12 0.148 N/A 1 0.059 47.0 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 12 0.177 N/A 1 0.059 47.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 2 0.237 N/A 0 9.6e-05 2.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.238 N/A 0 9.6e-05 2.0 PCs and sequencing center LOF
NG00065 European 2 0.271 N/A 0 9.6e-05 2.0 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 2 0.273 N/A 0 9.6e-05 2.0 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 73 0.414 N/A 0 0.039 822.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 73 0.449 N/A 0 0.039 822.9 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 2 0.548 N/A 0 9.6e-05 2.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 2 0.548 N/A 0 9.6e-05 2.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 73 0.651 N/A 0 0.039 822.9 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 77 0.653 N/A 0 0.040 869.9 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 77 0.662 N/A 0 0.040 869.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 77 0.665 N/A 1 0.040 869.9 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the UNC5C gene.

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The UNC5C gene contains 21,097 variants records (corresponding to 20,339 unique genomic positions).

The following variants, contained within ±100kb of UNC5C, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of UNC5C 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 N/A 3.3e-27 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 3.3e-27 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 3.3e-27 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.1e-22 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 1.1e-22 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 1.1e-22 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of UNC5C that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of UNC5C, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of UNC5C 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 UNC5C 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 UNC5C gene (chr4:96083655-96470357)

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:0033564 anterior/posterior axon guidance IEA
BP GO:0006915 apoptotic process IEA
BP GO:0007411 axon guidance IEA,TAS
BP GO:0007420 brain development TAS,IEA
BP GO:0007275 multicellular organism development IEA
BP GO:0038007 netrin-activated signaling pathway IEA
BP GO:0043065 positive regulation of apoptotic process IEA
BP GO:0030334 regulation of cell migration IEA
BP GO:0007165 signal transduction IEA
CC GO:0030054 cell junction IEA
CC GO:0016021 integral component of membrane IEA
CC GO:0016020 membrane IEA
CC GO:0043005 neuron projection IEA
CC GO:0005886 plasma membrane IEA
CC GO:0045202 synapse IEA
MF GO:0005042 netrin receptor activity IEA,TAS

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