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ACP2 - ENSG00000134575

acid phosphatase 2, lysosomal

Also known as: LAP

Location: chr11:47,260,853-47,270,457 reverse strand

Gene Type: protein coding

More information
NCBI Gene
53
HUGO
HGNC:123
Ensembl
ENSG00000134575
VEGA
OTTHUMG00000166949
OMIM
171650
UniProtKB
P11117

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 Meta 41 0.063 N/A 1 0.025 542.5 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 39 0.063 N/A 1 0.020 416.8 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 41 0.124 N/A 1 0.025 542.5 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 39 0.149 N/A 1 0.020 416.8 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 4 0.181 N/A 1 9.5e-03 7.5 PCs and sequencing center VEP MOD-HIGH
NG00065 Caribbean Hispanic 4 0.188 N/A 1 9.5e-03 7.5 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
NG00065 Meta 41 0.190 N/A 1 0.025 542.5 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 4 0.201 N/A 1 9.5e-03 7.5 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH
NG00065 European 39 0.292 N/A 1 0.020 416.8 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 1 0.369 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.369 N/A 0 1.3e-03 1.0 PCs and sequencing center LOF
NG00065 Meta 3 0.375 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 Caribbean Hispanic 1 0.384 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Caribbean Hispanic 1 0.384 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Caribbean Hispanic 1 0.391 N/A 0 1.3e-03 1.0 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 Caribbean Hispanic 1 0.391 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Meta 3 0.426 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 Meta 3 0.456 N/A 1 1.9e-04 4.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.579 N/A 1 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 2 0.579 N/A 1 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 VEP HIGH
NG00065 European 2 0.655 N/A 1 1.4e-04 3.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 2 0.655 N/A 1 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 2 0.675 N/A 1 1.4e-04 3.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.675 N/A 1 1.4e-04 3.0 PCs and sequencing center LOF

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the ACP2 gene.

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The ACP2 gene contains 915 variants records (corresponding to 845 unique genomic positions).

The following variants, contained within ±100kb of ACP2, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of ACP2 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
downstream N/A 6.0e-19 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 6.0e-19 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 6.0e-19 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 1.7e-15 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.7e-15 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 1.7e-15 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 7.0e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of ACP2 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of ACP2, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of ACP2 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 ACP2 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 ACP2 gene (chr11:47260853-47270457)

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:0016311 dephosphorylation IEA
BP GO:0007040 lysosome organization IEA
BP GO:0001501 skeletal system development IEA
CC GO:0070062 extracellular exosome IDA
CC GO:0016021 integral component of membrane TAS,IEA
CC GO:0043202 lysosomal lumen IEA
CC GO:0005765 lysosomal membrane IEA
CC GO:0005764 lysosome IEA,IDA
CC GO:0016020 membrane IDA,IEA
MF GO:0003993 acid phosphatase activity TAS,IEA
MF GO:0016787 hydrolase activity 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
Lysosome hsa04142
Metabolic pathways hsa01100
Riboflavin metabolism hsa00740