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.

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the RP11-78B10.2 gene.

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The RP11-78B10.2 gene contains 2,681 variants records (corresponding to 2,538 unique genomic positions).

The following variants, contained within ±100kb of RP11-78B10.2, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of RP11-78B10.2 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 9.0e-81 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 9.0e-81 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 9.0e-81 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.1e-63 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 1.1e-63 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene N/A 1.1e-63 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream A 5.7e-24 IGAP 2013: Stages 1 and 2 NG00036
downstream G 3.0e-23 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.7e-23 IGAP 2013: Stages 1 and 2 NG00036
downstream A 6.1e-23 IGAP 2013: Stages 1 and 2 NG00036
downstream A 6.9e-23 IGAP 2013: Stages 1 and 2 NG00036
upstream A 1.1e-22 IGAP 2013: Stages 1 and 2 NG00036
downstream T 1.3e-22 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.8e-22 IGAP 2013: Stages 1 and 2 NG00036
upstream T 3.1e-22 IGAP 2013: Stages 1 and 2 NG00036
downstream A 3.4e-22 IGAP 2013: Stages 1 and 2 NG00036
downstream A 5.0e-22 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.0e-21 IGAP 2013: Stages 1 and 2 NG00036
upstream A 8.3e-20 IGAP 2013: Stages 1 and 2 NG00036
upstream A 8.3e-20 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.7e-15 IGAP 2013: Stage 1 NG00036
in gene T 3.9e-15 IGAP 2013: Stage 1 NG00036
in gene T 4.1e-15 IGAP 2013: Stage 1 NG00036
upstream T 7.6e-15 IGAP 2013: Stage 1 NG00036
upstream A 7.7e-15 IGAP 2013: Stage 1 NG00036
downstream A 1.2e-14 IGAP 2013: Stage 1 NG00036
downstream A 1.9e-14 IGAP 2013: Stage 1 NG00036
upstream T 2.3e-14 IGAP 2013: Stage 1 NG00036
downstream G 2.6e-14 IGAP 2013: Stage 1 NG00036
downstream A 2.6e-14 IGAP 2013: Stage 1 NG00036
downstream C 2.6e-14 IGAP 2013: Stage 1 NG00036
downstream C 2.6e-14 IGAP 2013: Stage 1 NG00036
downstream T 2.7e-14 IGAP 2013: Stage 1 NG00036
downstream C 2.7e-14 IGAP 2013: Stage 1 NG00036
downstream T 2.8e-14 IGAP 2013: Stage 1 NG00036
downstream A 3.5e-14 IGAP 2013: Stage 1 NG00036
upstream A 3.5e-14 IGAP 2013: Stage 1 NG00036
downstream A 4.7e-14 IGAP 2013: Stage 1 NG00036
downstream A 4.9e-14 IGAP 2013: Stage 1 NG00036
downstream A 5.4e-14 IGAP 2013: Stage 1 NG00036
downstream A 7.3e-14 IGAP 2013: Stage 1 NG00036
downstream A 2.2e-13 IGAP 2013: Stage 1 NG00036
upstream A 6.8e-12 IGAP 2013: Stage 1 NG00036
upstream A 6.8e-12 IGAP 2013: Stage 1 NG00036
in gene T 8.1e-12 Transethnic LOAD: All Samples NG00056
upstream T 9.8e-12 Transethnic LOAD: All Samples NG00056
upstream A 1.0e-11 Transethnic LOAD: All Samples NG00056
upstream A 1.1e-11 Transethnic LOAD: All Samples NG00056
downstream A 3.1e-11 Transethnic LOAD: All Samples NG00056
upstream C 1.6e-10 IGAP 2013: Stages 1 and 2 NG00036
upstream T 2.5e-10 IGAP (2013): ADGC Subset NG00053
upstream T 2.8e-10 IGAP (2013): ADGC Subset NG00053
in gene T 3.0e-10 IGAP (2013): ADGC Subset NG00053
upstream A 3.4e-10 ADGC 2011: Stages 1 and 2 NG00027
downstream C 3.4e-10 IGAP 2013: Stage 1 NG00036
in gene T 4.5e-10 IGAP (2013): ADGC Subset NG00053
downstream A 4.6e-10 ADGC 2011: Stages 1 and 2 NG00027
downstream A 4.8e-10 ADGC 2011: Stages 1 and 2 NG00027
upstream A 4.9e-10 IGAP (2013): ADGC Subset NG00053
upstream A 5.4e-10 IGAP (2013): ADGC Subset NG00053
in gene A 6.2e-10 IGAP (2013): ADGC Subset NG00053
downstream A 1.1e-9 IGAP (2013): ADGC Subset NG00053
downstream A 1.5e-9 ADGC 2011: Stages 1 and 2 NG00027
downstream T 1.6e-9 ADGC 2011: Stages 1 and 2 NG00027
downstream A 1.8e-9 ADGC 2011: Stages 1 and 2 NG00027
downstream A 1.9e-9 IGAP (2013): ADGC Subset NG00053
downstream A 2.0e-9 Transethnic LOAD: All Samples NG00056
downstream A 2.2e-9 IGAP (2013): ADGC Subset NG00053
downstream C 2.6e-9 IGAP (2013): ADGC Subset NG00053
downstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
downstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
downstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
downstream T 2.8e-9 IGAP (2013): ADGC Subset NG00053
downstream A 2.8e-9 Transethnic LOAD: All Samples NG00056
downstream A 3.0e-9 Transethnic LOAD: All Samples NG00056
downstream A 3.1e-9 ADGC 2011: Stages 1 and 2 NG00027
downstream A 3.2e-9 IGAP (2013): ADGC Subset NG00053
in gene A 3.3e-9 Transethnic LOAD: All Samples NG00056
downstream A 4.0e-9 IGAP (2013): ADGC Subset NG00053
downstream A 4.5e-9 IGAP (2013): ADGC Subset NG00053
downstream A 4.8e-9 IGAP (2013): ADGC Subset NG00053
downstream A 5.7e-9 IGAP (2013): ADGC Subset NG00053
downstream A 6.3e-9 Transethnic LOAD: All Samples NG00056
in gene T 7.4e-9 Transethnic LOAD: All Samples NG00056
downstream A 7.9e-9 IGAP (2013): ADGC Subset NG00053
upstream T 1.0e-8 Transethnic LOAD: All Samples NG00056
downstream A 1.1e-8 Transethnic LOAD: All Samples NG00056
upstream T 1.3e-8 Transethnic LOAD: All Samples NG00056
downstream A 1.4e-8 ADGC 2011: Stage 1 NG00027
downstream A 1.5e-8 ADGC 2011: Stage 1 NG00027
upstream A 1.9e-8 ADGC 2011: Stage 1 NG00027
downstream A 2.1e-8 Transethnic LOAD: All Samples NG00056
downstream A 2.3e-8 IGAP (2013): ADGC Subset NG00053
upstream A 2.7e-8 Transethnic LOAD: All Samples NG00056
upstream A 2.7e-8 Transethnic LOAD: All Samples NG00056
downstream C 2.8e-8 Transethnic LOAD: All Samples NG00056
downstream A 2.9e-8 Transethnic LOAD: All Samples NG00056
downstream T 3.1e-8 Transethnic LOAD: All Samples NG00056
upstream A 3.3e-8 ADGC 2011: Adjusted Stages 1 and 2 NG00027
downstream A 4.2e-8 Transethnic LOAD: All Samples NG00056
downstream A 4.3e-8 ADGC 2011: Stage 1 NG00027
downstream T 4.3e-8 ADGC 2011: Stage 1 NG00027
downstream A 4.4e-8 Transethnic LOAD: All Samples NG00056
downstream A 4.7e-8 ADGC 2011: Stage 1 NG00027
downstream A 5.0e-8 ADGC 2011: Adjusted Stages 1 and 2 NG00027

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of RP11-78B10.2 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of RP11-78B10.2, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of RP11-78B10.2 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 RP11-78B10.2 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 RP11-78B10.2 gene (chr1:207725270-207779900)

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.

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.