BIN1 - ENSG00000136717

bridging integrator 1

Also known as: SH3P9, AMPH2

Location: chr2:127,805,603-127,864,931 reverse strand

Gene Type: protein coding

More information
NCBI Gene
274
HUGO
HGNC:1052
Ensembl
ENSG00000136717
VEGA
OTTHUMG00000131465
OMIM
601248
UniProtKB
O00499

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.

To add tracks, use the provided link to switch to the full genome browser view.

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 3 0.359 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 European 3 0.359 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 European 3 0.420 N/A 0 6.7e-04 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 HIGH N/A
NG00065 European 3 0.420 N/A 0 6.7e-04 14.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 European 3 0.645 N/A 0 6.7e-04 14.0 PCs and sequencing center LOF N/A
NG00065 European 3 0.645 N/A 0 6.7e-04 14.0 PCs and sequencing center VEP HIGH N/A
NG00065 European 53 0.655 N/A 1 0.019 387.2 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 54 0.684 N/A 1 0.020 428.3 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 6 0.929 N/A 1 0.052 41.1 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 6 0.936 N/A 1 0.052 41.1 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 6 0.937 N/A 1 0.052 41.1 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 53 0.964 N/A 1 0.019 387.2 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 Meta 54 0.982 N/A 1 0.020 428.3 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 54 0.992 N/A 0 0.020 428.3 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 53 0.996 N/A 0 0.019 387.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the BIN1 gene.

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The BIN1 gene contains 4,152 variants records (corresponding to 3,980 unique genomic positions).

The following variants, contained within ±100kb of BIN1, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of BIN1 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 T 6.9e-44 IGAP 2013: Stages 1 and 2 NG00036
downstream T 5.4e-28 IGAP 2013: Stages 1 and 2 NG00036
downstream G 3.1e-27 IGAP 2013: Stages 1 and 2 NG00036
downstream A 3.8e-27 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.0e-26 IGAP 2013: Stage 1 NG00036
downstream T 1.7e-26 IGAP 2013: Stage 1 NG00036
in gene A 1.1e-25 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.6e-25 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.5e-21 IGAP 2013: Stages 1 and 2 NG00036
in gene T 6.1e-18 IGAP 2013: Stages 1 and 2 NG00036
downstream A 6.5e-18 IGAP 2013: Stage 1 NG00036
downstream G 2.2e-17 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.3e-17 Transethnic LOAD: All Samples NG00056
downstream T 3.9e-17 IGAP (2013): ADGC Subset NG00053
downstream A 4.0e-17 IGAP 2013: Stages 1 and 2 NG00036
downstream T 5.1e-17 IGAP 2013: Stage 1 NG00036
downstream A 6.0e-17 IGAP (2013): ADGC Subset NG00053
downstream C 6.4e-17 IGAP 2013: Stage 1 NG00036
downstream T 2.0e-16 IGAP 2013: Stages 1 and 2 NG00036
downstream G 2.1e-16 IGAP 2013: Stage 1 NG00036
downstream T 3.6e-16 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.7e-16 IGAP 2013: Stage 1 NG00036
downstream C 7.5e-16 IGAP 2013: Stages 1 and 2 NG00036
downstream A 8.9e-16 Transethnic LOAD: All Samples NG00056
downstream C 1.3e-15 IGAP 2013: Stages 1 and 2 NG00036
downstream C 9.8e-15 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.2e-14 ADGC 2011: Stages 1 and 2 NG00027
downstream G 4.5e-14 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.6e-14 ADGC 2011: Stages 1 and 2 NG00027
downstream G 7.4e-14 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.0e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream G 1.1e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.1e-13 IGAP (2013): ADGC Subset NG00053
downstream A 1.5e-13 ADGC 2011: Adjusted Stages 1 and 2 NG00027
downstream A 1.5e-13 ADGC 2011: Adjusted Stages 1 and 2 NG00027
downstream T 1.6e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream G 1.7e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.7e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 2.1e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.1e-13 Transethnic LOAD: All Samples NG00056
downstream G 2.3e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.5e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.8e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.9e-13 Transethnic LOAD: All Samples NG00056
downstream C 3.2e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 3.2e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.4e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 3.8e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.9e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.7e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 4.9e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream C 4.9e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 5.4e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 5.4e-13 Transethnic LOAD: All Samples NG00056
downstream G 5.5e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene T 7.6e-13 IGAP 2013: Stage 1 NG00036
downstream C 7.7e-13 IGAP 2013: Stage 1 NG00036
downstream C 7.8e-13 IGAP 2013: Stage 1 NG00036
downstream T 7.9e-13 IGAP 2013: Stage 1 NG00036
downstream T 7.9e-13 IGAP 2013: Stage 1 NG00036
in gene A 8.1e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream G 8.9e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.2e-12 Transethnic LOAD: All Samples NG00056
downstream T 1.5e-12 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.7e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.5e-12 IGAP (2013): ADGC Subset NG00053
downstream A 2.6e-12 ADGC 2011: Stages 1 and 2 NG00027
in gene A 2.6e-12 IGAP 2013: Stage 1 NG00036
downstream C 2.7e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream C 2.9e-12 IGAP 2013: Stage 1 NG00036
downstream T 3.0e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.1e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream A 3.4e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream A 3.9e-12 ADGC 2011: Adjusted Stages 1 and 2 NG00027
in gene A 7.4e-12 IGAP (2013): ADGC Subset NG00053
downstream A 7.8e-12 IGAP (2013): ADGC Subset NG00053
downstream T 1.7e-11 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.5e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.5e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.6e-11 ADGC 2011: Adjusted Stage 1 NG00027
downstream A 2.8e-11 ADGC 2011: Adjusted Stage 1 NG00027
downstream A 2.9e-11 ADGC 2011: Stage 1 NG00027
downstream A 3.1e-11 Transethnic LOAD: All Samples NG00056
downstream T 3.1e-11 Transethnic LOAD: All Samples NG00056
downstream A 3.1e-11 ADGC 2011: Stage 1 NG00027
in gene T 3.2e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.4e-11 Transethnic LOAD: All Samples NG00056
downstream A 3.7e-11 IGAP (2013): ADGC Subset NG00053
downstream T 4.9e-11 Transethnic LOAD: All Samples NG00056
in gene C 5.4e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream A 7.2e-11 IGAP 2013: Stage 1 NG00036
in gene T 7.4e-11 Transethnic LOAD: All Samples NG00056
downstream A 7.7e-11 Transethnic LOAD: All Samples NG00056
downstream A 8.3e-11 Transethnic LOAD: All Samples NG00056
downstream A 1.2e-10 ADGC 2011: Adjusted Stage 1 NG00027
downstream A 1.3e-10 IGAP 2013: Stage 1 NG00036
downstream G 1.3e-10 IGAP 2013: Stage 1 NG00036
downstream A 1.6e-10 Transethnic LOAD: All Samples NG00056
downstream A 1.9e-10 IGAP 2013: Stage 1 NG00036
downstream A 3.0e-10 ADGC 2011: Stage 1 NG00027
in gene T 3.9e-10 AD Age of Onset Survival (IGAP) NG00058
downstream C 4.7e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene A 5.2e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream A 5.3e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream T 5.3e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream A 6.1e-10 Transethnic LOAD: All Samples NG00056
in gene A 6.8e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream A 8.3e-10 IGAP 2013: Stages 1 and 2 NG00036
in gene T 8.5e-10 IGAP (2013): ADGC Subset NG00053
in gene N/A C 8.9e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream A 9.4e-10 Transethnic LOAD: All Samples NG00056
downstream A 1.2e-9 Transethnic LOAD: All Samples NG00056
downstream T 1.2e-9 Transethnic LOAD: All Samples NG00056
in gene C 1.2e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.2e-9 Transethnic LOAD: All Samples NG00056
downstream T 1.4e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream G 1.6e-9 IGAP 2013: Stage 1 NG00036
downstream A 1.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.9e-9 Transethnic LOAD: All Samples NG00056
downstream C 2.1e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 2.2e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.2e-9 IGAP (2013): ADGC Subset NG00053
downstream G 2.3e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 2.4e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.6e-9 Transethnic LOAD: All Samples NG00056
downstream C 2.6e-9 Transethnic LOAD: All Samples NG00056
downstream A 2.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 2.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.9e-9 IGAP 2013: Stage 1 NG00036
in gene C 3.0e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene N/A C 3.6e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene T 3.7e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene A 4.2e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 4.2e-9 IGAP 2013: Stage 1 NG00036
downstream A 4.7e-9 Transethnic LOAD: APOE e4 Non-Carriers NG00056
in gene T 5.4e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream C 6.0e-9 Transethnic LOAD: APOE e4 Non-Carriers NG00056
in gene C 6.2e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 6.5e-9 IGAP 2013: Stage 1 NG00036
downstream T 6.6e-9 IGAP 2013: Stage 1 NG00036
in gene T 6.6e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream C 6.8e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 6.9e-9 Transethnic LOAD: All Samples NG00056
downstream C 7.2e-9 IGAP 2013: Stage 1 NG00036
downstream C 7.2e-9 IGAP 2013: Stage 1 NG00036
downstream T 7.2e-9 IGAP 2013: Stage 1 NG00036
in gene T 7.2e-9 AD Age of Onset Survival (IGAP) NG00058
downstream A 7.9e-9 Transethnic LOAD: APOE e4 Non-Carriers NG00056
in gene A 8.0e-9 AD Age of Onset Survival (IGAP) NG00058
in gene A 8.1e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 8.3e-9 AD Age of Onset Survival (IGAP) NG00058
downstream A 8.9e-9 IGAP (2013): ADGC Subset NG00053
downstream A 8.9e-9 IGAP (2013): ADGC Subset NG00053
downstream C 9.0e-9 IGAP 2013: Stage 1 NG00036
in gene T 9.1e-9 IGAP 2013: Stage 1 NG00036
downstream T 9.2e-9 Transethnic LOAD: APOE e4 Non-Carriers NG00056
downstream A 9.2e-9 Transethnic LOAD: All Samples NG00056
in gene A 1.1e-8 Transethnic LOAD: APOE e4 Non-Carriers NG00056
downstream A 1.1e-8 AD Age of Onset Survival (IGAP) NG00058
downstream A 1.2e-8 Transethnic LOAD: All Samples NG00056
downstream A 1.2e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 1.2e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 1.3e-8 AD Age of Onset Survival (IGAP) NG00058
in gene T 1.3e-8 AD Age of Onset Survival (IGAP) NG00058
in gene T 1.3e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 1.4e-8 Transethnic LOAD: All Samples NG00056
downstream T 1.4e-8 Transethnic LOAD: All Samples NG00056
downstream A 1.4e-8 IGAP 2013: Stage 1 NG00036
downstream A 1.5e-8 IGAP 2013: Stage 1 NG00036
downstream A 1.5e-8 AD Age of Onset Survival (IGAP) NG00058
downstream A 1.5e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 1.7e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 1.8e-8 Transethnic LOAD: All Samples NG00056
in gene T 1.8e-8 Transethnic LOAD: All Samples NG00056
downstream A 2.0e-8 Transethnic LOAD: APOE e4 Non-Carriers NG00056
downstream C 2.1e-8 IGAP 2013: Stage 1 NG00036
downstream A 2.2e-8 IGAP (2013): ADGC Subset NG00053
downstream C 2.2e-8 Transethnic LOAD: All Samples NG00056
downstream T 2.2e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 2.5e-8 AD Age of Onset Survival (IGAP) NG00058
downstream A 2.6e-8 IGAP (2013): ADGC Subset NG00053
downstream T 2.6e-8 AD Age of Onset Survival (IGAP) NG00058
in gene C 2.6e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.0e-8 Transethnic LOAD: APOE e4 Non-Carriers NG00056
downstream A 3.1e-8 IGAP (2013): ADGC Subset NG00053
downstream T 3.4e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 3.5e-8 AD Age of Onset Survival (IGAP) NG00058
downstream A 3.6e-8 Transethnic LOAD: All Samples NG00056
downstream T 3.7e-8 IGAP 2013: Stage 1 NG00036
downstream A 3.8e-8 IGAP 2013: Stage 1 NG00036
downstream T 3.9e-8 IGAP 2013: Stage 1 NG00036
downstream A 4.0e-8 IGAP (2013): ADGC Subset NG00053
downstream T 4.0e-8 IGAP (2013): ADGC Subset NG00053
downstream T 4.0e-8 IGAP (2013): ADGC Subset NG00053
downstream T 4.0e-8 IGAP (2013): ADGC Subset NG00053
downstream A 4.2e-8 IGAP 2013: Stage 1 NG00036
in gene T 4.3e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.4e-8 AD Age of Onset Survival (IGAP) NG00058
downstream T 4.4e-8 AD Age of Onset Survival (IGAP) NG00058
downstream A 4.4e-8 IGAP (2013): ADGC Subset NG00053
downstream A 4.5e-8 IGAP 2013: Stage 1 NG00036
downstream A 4.8e-8 Transethnic LOAD: All Samples NG00056

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of BIN1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of BIN1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of BIN1 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 BIN1 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 BIN1 gene (chr2:127805603-127864931)

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:0030154 cell differentiation IEA
BP GO:0008283 cell proliferation TAS
BP GO:0006897 endocytosis IEA
BP GO:0060988 lipid tube assembly IMP
BP GO:0061024 membrane organization TAS
BP GO:0007275 multicellular organism development IEA
BP GO:0042692 muscle cell differentiation IEA
BP GO:0051647 nucleus localization IEA
BP GO:0006997 nucleus organization IMP
BP GO:0043065 positive regulation of apoptotic process IMP,IDA
BP GO:0048711 positive regulation of astrocyte differentiation IMP
BP GO:0071156 regulation of cell cycle arrest IDA
BP GO:0030100 regulation of endocytosis IEA
BP GO:0045664 regulation of neuron differentiation IMP
BP GO:0016032 viral process IEA
CC GO:0015629 actin cytoskeleton TAS
CC GO:0030424 axon IDA
CC GO:0043194 axon initial segment ISS
CC GO:0005737 cytoplasm IDA,IEA
CC GO:0005829 cytosol IDA,TAS
CC GO:0031674 I band ISS
CC GO:0060987 lipid tube IMP
CC GO:0016020 membrane IDA
CC GO:0033268 node of Ranvier ISS
CC GO:0005635 nuclear envelope IEA
CC GO:0005634 nucleus IEA
CC GO:0030315 T-tubule ISS
CC GO:0030018 Z disc ISS
MF GO:0051015 actin filament binding IDA
MF GO:0042802 identical protein binding IPI
MF GO:0005515 protein binding IPI
MF GO:0070063 RNA polymerase binding IPI
MF GO:0048156 tau protein binding IPI,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
Endocytosis hsa04144
Fc gamma R-mediated phagocytosis hsa04666