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 European 54 0.163 N/A 0 0.010 218.4 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 61 0.279 N/A 0 0.011 248.4 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 9 0.332 N/A 1 0.038 30.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 9 0.376 N/A 1 0.038 30.0 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 9 0.385 N/A 1 0.038 30.0 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 4 0.491 N/A 1 1.9e-04 4.0 PCs and sequencing center VEP HIGH
NG00065 European 4 0.491 N/A 1 1.9e-04 4.0 PCs and sequencing center LOF
NG00065 European 4 0.752 N/A 1 1.9e-04 4.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 4 0.752 N/A 1 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 4 0.757 N/A 1 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 4 0.757 N/A 1 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 VEP HIGH
NG00065 European 54 0.849 N/A 1 0.010 218.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 61 0.872 N/A 1 0.011 248.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 54 0.920 N/A 1 0.010 218.4 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 61 0.930 N/A 1 0.011 248.4 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the CD2AP gene.

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The CD2AP gene contains 8,161 variants records (corresponding to 7,798 unique genomic positions).

The following variants, contained within ±100kb of CD2AP, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of CD2AP 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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Login in to select variants and add them to your basket.

Relative Position Variant ADSP? Allele p-Value Track Accession
downstream N/A 1.1e-45 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 1.1e-45 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 1.1e-45 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 2.6e-45 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 2.6e-45 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 2.6e-45 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 6.5e-18 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 6.5e-18 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 6.5e-18 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 2.6e-15 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 2.6e-15 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene N/A 2.6e-15 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene G 5.2e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream C 5.6e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream G 5.8e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene C 6.0e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream T 6.2e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene T 6.2e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene G 6.3e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream A 6.9e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene G 7.4e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene A 7.6e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream T 7.6e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream A 7.9e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene G 8.1e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene G 8.2e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream C 8.9e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream C 9.0e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.1e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.1e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.3e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.4e-10 IGAP 2013: Stages 1 and 2 NG00036
upstream A 1.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 1.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.7e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.8e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 1.9e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.9e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 2.0e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 2.3e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 2.3e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 2.4e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 2.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 2.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 2.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 2.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 2.6e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.7e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 3.1e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 3.1e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene C 3.3e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.5e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.7e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 3.8e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene G 4.4e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream T 9.4e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.5e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream G 3.5e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream T 4.0e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream C 5.3e-9 IGAP 2013: Stage 1 NG00036
downstream G 6.4e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 7.4e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream A 9.1e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream C 9.5e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.3e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream C 1.3e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 1.4e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene G 3.1e-8 IGAP 2013: Stage 1 NG00036
upstream C 3.3e-8 IGAP 2013: Stage 1 NG00036
in gene C 3.6e-8 IGAP 2013: Stage 1 NG00036
in gene G 3.7e-8 IGAP 2013: Stage 1 NG00036
in gene T 3.8e-8 IGAP 2013: Stage 1 NG00036
in gene G 3.9e-8 IGAP 2013: Stage 1 NG00036
in gene T 4.0e-8 IGAP 2013: Stage 1 NG00036
in gene G 4.2e-8 IGAP 2013: Stage 1 NG00036
downstream T 4.2e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream G 4.5e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream T 4.5e-8 IGAP 2013: Stage 1 NG00036
in gene A 4.6e-8 IGAP 2013: Stage 1 NG00036
in gene G 4.7e-8 IGAP 2013: Stage 1 NG00036
in gene A 4.8e-8 IGAP 2013: Stage 1 NG00036
in gene A 4.8e-8 IGAP 2013: Stage 1 NG00036
in gene G 4.9e-8 IGAP 2013: Stage 1 NG00036
upstream T 4.9e-8 IGAP 2013: Stage 1 NG00036
in gene G 4.9e-8 IGAP 2013: Stage 1 NG00036
in gene C 4.9e-8 IGAP 2013: Stage 1 NG00036
in gene T 5.0e-8 IGAP 2013: Stage 1 NG00036
in gene T 5.0e-8 IGAP 2013: Stage 1 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of CD2AP that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of CD2AP, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of CD2AP 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 CD2AP 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 CD2AP gene (chr6:47445525-47594999)

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:0007049 cell cycle IEA
BP GO:0051301 cell division IEA
BP GO:0016477 cell migration IEA
BP GO:0007010 cytoskeleton organization IEA
BP GO:0007067 mitotic nuclear division IEA
BP GO:0032911 negative regulation of transforming growth factor beta1 production IEA
BP GO:1900182 positive regulation of protein localization to nucleus IEA
BP GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IEA
BP GO:0006461 protein complex assembly TAS
BP GO:2000249 regulation of actin cytoskeleton reorganization IEA
BP GO:0048259 regulation of receptor-mediated endocytosis IEA
BP GO:0007165 signal transduction NAS
BP GO:0016337 single organismal cell-cell adhesion IEA
BP GO:0006930 substrate-dependent cell migration, cell extension TAS
BP GO:0016050 vesicle organization IEA
CC GO:0015629 actin cytoskeleton TAS
CC GO:0005913 cell-cell adherens junction IDA
CC GO:0005911 cell-cell junction IEA
CC GO:0031252 cell leading edge IEA
CC GO:0042995 cell projection IEA
CC GO:0005737 cytoplasm TAS,IEA
CC GO:0005856 cytoskeleton IEA
CC GO:0030139 endocytic vesicle IEA
CC GO:0070062 extracellular exosome IDA
CC GO:0031941 filamentous actin IDA
CC GO:0048471 perinuclear region of cytoplasm IEA
CC GO:0005886 plasma membrane IEA
CC GO:0043234 protein complex IEA
CC GO:0001726 ruffle IDA,IEA
MF GO:0008013 beta-catenin binding IEA
MF GO:0045296 cadherin binding IEA
MF GO:0098641 cadherin binding involved in cell-cell adhesion IDA
MF GO:0005515 protein binding IPI
MF GO:0032403 protein complex binding IEA
MF GO:0008022 protein C-terminus binding IEA
MF GO:0017124 SH3 domain binding IPI,IEA
MF GO:0005200 structural constituent of cytoskeleton TAS
MF GO:0005172 vascular endothelial growth factor receptor 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
Bacterial invasion of epithelial cells hsa05100