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 62 5.1e-03 N/A 1 0.035 734.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 66 9.0e-03 N/A 0 0.038 833.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 62 0.017 N/A 1 0.035 734.0 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 66 0.023 N/A 0 0.038 833.0 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 62 0.025 N/A 1 0.035 734.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 66 0.034 N/A 0 0.038 833.0 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 18 0.436 N/A 1 0.201 159.0 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 18 0.440 N/A 1 0.201 159.0 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 18 0.460 N/A 1 0.201 159.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 9 0.666 N/A 1 8.1e-04 17.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 European 9 0.666 N/A 1 8.1e-04 17.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 European 9 0.709 N/A 1 8.1e-04 17.0 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 9 0.709 N/A 1 8.1e-04 17.0 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 9 0.843 N/A 1 8.1e-04 17.0 PCs and sequencing center VEP HIGH N/A
NG00065 European 9 0.843 N/A 1 8.1e-04 17.0 PCs and sequencing center LOF N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the CR1L gene.

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The CR1L gene contains 5,490 variants records (corresponding to 5,263 unique genomic positions).

The following variants, contained within ±100kb of CR1L, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of CR1L 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
upstream N/A 9.0e-81 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 9.0e-81 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 9.0e-81 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
upstream N/A 1.1e-63 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 1.1e-63 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
upstream N/A 1.1e-63 ADSP Single-Variant Risk Association: European (Model 2) NG00065
upstream G 3.0e-23 IGAP 2013: Stages 1 and 2 NG00036
upstream A 4.7e-23 IGAP 2013: Stages 1 and 2 NG00036
upstream A 6.1e-23 IGAP 2013: Stages 1 and 2 NG00036
upstream A 6.9e-23 IGAP 2013: Stages 1 and 2 NG00036
upstream T 1.3e-22 IGAP 2013: Stages 1 and 2 NG00036
upstream A 2.8e-22 IGAP 2013: Stages 1 and 2 NG00036
upstream A 3.4e-22 IGAP 2013: Stages 1 and 2 NG00036
upstream A 5.0e-22 IGAP 2013: Stages 1 and 2 NG00036
upstream C 1.0e-21 IGAP 2013: Stages 1 and 2 NG00036
upstream A 3.7e-15 IGAP 2013: Stage 1 NG00036
upstream T 3.9e-15 IGAP 2013: Stage 1 NG00036
upstream T 4.1e-15 IGAP 2013: Stage 1 NG00036
upstream A 1.2e-14 IGAP 2013: Stage 1 NG00036
upstream A 1.9e-14 IGAP 2013: Stage 1 NG00036
upstream G 2.6e-14 IGAP 2013: Stage 1 NG00036
upstream A 2.6e-14 IGAP 2013: Stage 1 NG00036
upstream C 2.6e-14 IGAP 2013: Stage 1 NG00036
upstream C 2.6e-14 IGAP 2013: Stage 1 NG00036
upstream T 2.7e-14 IGAP 2013: Stage 1 NG00036
upstream C 2.7e-14 IGAP 2013: Stage 1 NG00036
upstream T 2.8e-14 IGAP 2013: Stage 1 NG00036
upstream A 3.5e-14 IGAP 2013: Stage 1 NG00036
upstream A 4.7e-14 IGAP 2013: Stage 1 NG00036
upstream A 4.9e-14 IGAP 2013: Stage 1 NG00036
upstream A 5.4e-14 IGAP 2013: Stage 1 NG00036
upstream A 7.3e-14 IGAP 2013: Stage 1 NG00036
upstream A 2.2e-13 IGAP 2013: Stage 1 NG00036
upstream T 8.1e-12 Transethnic LOAD: All Samples NG00056
upstream A 3.1e-11 Transethnic LOAD: All Samples NG00056
upstream T 3.0e-10 IGAP (2013): ADGC Subset NG00053
in gene C 3.4e-10 IGAP 2013: Stage 1 NG00036
upstream T 4.5e-10 IGAP (2013): ADGC Subset NG00053
upstream A 4.6e-10 ADGC 2011: Stages 1 and 2 NG00027
upstream A 4.8e-10 ADGC 2011: Stages 1 and 2 NG00027
upstream A 6.2e-10 IGAP (2013): ADGC Subset NG00053
upstream A 1.1e-9 IGAP (2013): ADGC Subset NG00053
upstream A 1.5e-9 ADGC 2011: Stages 1 and 2 NG00027
upstream T 1.6e-9 ADGC 2011: Stages 1 and 2 NG00027
upstream A 1.8e-9 ADGC 2011: Stages 1 and 2 NG00027
upstream A 1.9e-9 IGAP (2013): ADGC Subset NG00053
upstream A 2.0e-9 Transethnic LOAD: All Samples NG00056
upstream A 2.2e-9 IGAP (2013): ADGC Subset NG00053
upstream C 2.6e-9 IGAP (2013): ADGC Subset NG00053
upstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
upstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
upstream T 2.6e-9 IGAP (2013): ADGC Subset NG00053
upstream T 2.8e-9 IGAP (2013): ADGC Subset NG00053
upstream A 2.8e-9 Transethnic LOAD: All Samples NG00056
upstream A 3.0e-9 Transethnic LOAD: All Samples NG00056
upstream A 3.1e-9 ADGC 2011: Stages 1 and 2 NG00027
upstream A 3.2e-9 IGAP (2013): ADGC Subset NG00053
upstream A 3.3e-9 Transethnic LOAD: All Samples NG00056
upstream A 4.0e-9 IGAP (2013): ADGC Subset NG00053
upstream A 4.5e-9 IGAP (2013): ADGC Subset NG00053
upstream A 4.8e-9 IGAP (2013): ADGC Subset NG00053
upstream A 5.7e-9 IGAP (2013): ADGC Subset NG00053
upstream A 6.3e-9 Transethnic LOAD: All Samples NG00056
upstream T 7.4e-9 Transethnic LOAD: All Samples NG00056
upstream A 7.9e-9 IGAP (2013): ADGC Subset NG00053
upstream A 1.1e-8 Transethnic LOAD: All Samples NG00056
upstream A 1.4e-8 ADGC 2011: Stage 1 NG00027
upstream A 1.5e-8 ADGC 2011: Stage 1 NG00027
upstream A 2.1e-8 Transethnic LOAD: All Samples NG00056
upstream A 2.3e-8 IGAP (2013): ADGC Subset NG00053
upstream C 2.8e-8 Transethnic LOAD: All Samples NG00056
upstream A 2.9e-8 Transethnic LOAD: All Samples NG00056
upstream T 3.1e-8 Transethnic LOAD: All Samples NG00056
upstream A 4.2e-8 Transethnic LOAD: All Samples NG00056
upstream A 4.3e-8 ADGC 2011: Stage 1 NG00027
upstream T 4.3e-8 ADGC 2011: Stage 1 NG00027
upstream A 4.4e-8 Transethnic LOAD: All Samples NG00056
upstream A 4.7e-8 ADGC 2011: Stage 1 NG00027
upstream A 5.0e-8 ADGC 2011: Adjusted Stages 1 and 2 NG00027

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of CR1L that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of CR1L, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of CR1L 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 CR1L 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 CR1L gene (chr1:207818458-207911761)

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
CC GO:0005737 cytoplasm IEA
CC GO:0005576 extracellular region IEA
CC GO:0016020 membrane IEA
CC GO:0043235 receptor complex IDA

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.