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 European 123 0.012 N/A 1 0.026 535.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 129 0.017 N/A 1 0.029 637.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 123 0.049 N/A 1 0.026 535.7 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 123 0.055 N/A 1 0.026 535.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 129 0.072 N/A 1 0.029 637.0 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 129 0.078 N/A 1 0.029 637.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 3 0.121 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 3 0.183 N/A 0 1.4e-04 3.0 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 5 0.246 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 European 3 0.348 N/A 0 1.4e-04 3.0 PCs and sequencing center LOF
NG00065 European 5 0.366 N/A 0 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 5 0.398 N/A 0 2.4e-04 5.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 18 0.859 N/A 0 0.128 101.3 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 18 0.875 N/A 0 0.128 101.3 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 18 0.880 N/A 0 0.128 101.3 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the RIN3 gene.

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The RIN3 gene contains 10,634 variants records (corresponding to 10,168 unique genomic positions).

The following variants, contained within ±100kb of RIN3, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of RIN3 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
upstream N/A 9.7e-11 ADSP Single-Variant Risk Association: European (Model 2) NG00065
upstream N/A 9.7e-11 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 9.7e-11 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
upstream T 5.5e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream C 1.1e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 4.1e-8 IGAP 2013: Stage 1 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of RIN3 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of RIN3, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of RIN3 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 RIN3 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 RIN3 gene (chr14:92980118-93155339)

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:0006897 endocytosis NAS
BP GO:0061024 membrane organization TAS
BP GO:0043547 positive regulation of GTPase activity IEA
BP GO:0007165 signal transduction IEA
CC GO:0005737 cytoplasm IEA
CC GO:0031410 cytoplasmic vesicle IDA,IEA
CC GO:0005829 cytosol TAS
CC GO:0005769 early endosome IEA,IDA
CC GO:0005768 endosome IEA
MF GO:0005096 GTPase activator activity IEA
MF GO:0005515 protein binding IPI
MF GO:0017137 Rab GTPase binding IDA
MF GO:0017112 Rab guanyl-nucleotide exchange factor activity TAS,IMP

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.