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POLR2E - ENSG00000099817

RNA polymerase II subunit E

Also known as: RPB5, RPABC1, XAP4, hRPB25, hsRPB5

Location: chr19:1,086,594-1,095,598 reverse strand

Gene Type: protein coding

More information
NCBI Gene
5434
HUGO
HGNC:9192
Ensembl
ENSG00000099817
VEGA
OTTHUMG00000181873
OMIM
180664
UniProtKB
P19388

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 2 0.033 N/A 0 2.6e-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 LOF
NG00065 European 2 0.033 N/A 0 2.6e-04 5.4 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 0.036 N/A 0 2.6e-04 5.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 2 0.036 N/A 0 2.6e-04 5.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 18 0.039 N/A 1 3.4e-03 71.8 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 18 0.041 N/A 0 3.4e-03 72.8 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 18 0.043 N/A 1 3.4e-03 71.8 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 Meta 18 0.046 N/A 0 3.4e-03 72.8 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 European 18 0.051 N/A 1 3.4e-03 71.8 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 18 0.056 N/A 0 3.4e-03 72.8 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 1 0.218 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 MOD-HIGH
NG00065 Caribbean Hispanic 1 0.221 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP MOD-HIGH
NG00065 Caribbean Hispanic 1 0.237 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 MOD-HIGH
NG00065 European 2 0.613 N/A 0 2.6e-04 5.4 PCs and sequencing center VEP HIGH
NG00065 European 2 0.613 N/A 0 2.6e-04 5.0 PCs and sequencing center LOF

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the POLR2E gene.

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The POLR2E gene contains 1,275 variants records (corresponding to 1,169 unique genomic positions).

The following variants, contained within ±100kb of POLR2E, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of POLR2E 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 6.0e-25 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 6.0e-25 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 6.0e-25 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 8.2e-20 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 8.2e-20 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 8.2e-20 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 4.4e-17 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 4.4e-17 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene N/A 4.4e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 8.6e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 8.6e-17 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 8.6e-17 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream A 1.1e-15 IGAP 2013: Stages 1 and 2 NG00036
upstream G 1.4e-15 IGAP 2013: Stages 1 and 2 NG00036
in gene N/A 1.2e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 1.2e-14 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 1.2e-14 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
upstream G 4.2e-13 IGAP 2013: Stages 1 and 2 NG00036
upstream G 5.2e-13 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
upstream G 1.9e-12 IGAP 2013: Stages 1 and 2 NG00036
upstream A 5.5e-12 IGAP 2013: Stages 1 and 2 NG00036
upstream T 4.9e-11 IGAP 2013: Stages 1 and 2 NG00036
upstream A 4.5e-10 IGAP 2013: Stages 1 and 2 NG00036
upstream T 7.8e-10 IGAP 2013: Stages 1 and 2 NG00036
upstream C 1.3e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream G 1.5e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream A 1.7e-9 IGAP 2013: Stage 1 NG00036
upstream C 1.7e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream A 1.9e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream A 2.2e-9 ADGC African Americans 2013: APOE Adj NG00039
upstream A 2.3e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream T 2.9e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream G 4.3e-9 IGAP 2013: Stage 1 NG00036
upstream A 4.7e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream A 4.7e-9 IGAP 2013: Stage 1 NG00036
upstream C 9.2e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream G 1.2e-8 IGAP 2013: Stage 1 NG00036
upstream G 1.3e-8 IGAP 2013: Stage 1 NG00036
upstream G 1.3e-8 IGAP 2013: Stage 1 NG00036
upstream G 1.5e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream T 1.7e-8 IGAP 2013: Stage 1 NG00036
upstream A 1.8e-8 IGAP 2013: Stage 1 NG00036
upstream G 2.0e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A 2.0e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 2.0e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 2.0e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
upstream A 3.1e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream T 3.1e-8 ADGC African Americans 2013: APOE Adj NG00039

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of POLR2E that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of POLR2E, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of POLR2E 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 POLR2E 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 POLR2E gene (chr19:1086594-1095598)

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:0006370 7-methylguanosine mRNA capping TAS
BP GO:0008543 fibroblast growth factor receptor signaling pathway TAS
BP GO:0010467 gene expression TAS
BP GO:0031047 gene silencing by RNA TAS
BP GO:0000398 mRNA splicing, via spliceosome TAS
BP GO:0045815 positive regulation of gene expression, epigenetic TAS
BP GO:0032481 positive regulation of type I interferon production TAS
BP GO:0050434 positive regulation of viral transcription TAS
BP GO:0042795 snRNA transcription from RNA polymerase II promoter TAS
BP GO:0035019 somatic stem cell population maintenance TAS
BP GO:0006363 termination of RNA polymerase I transcription TAS
BP GO:0006283 transcription-coupled nucleotide-excision repair TAS
BP GO:0006351 transcription, DNA-templated IEA
BP GO:0006368 transcription elongation from RNA polymerase II promoter TAS
BP GO:0006362 transcription elongation from RNA polymerase I promoter TAS
BP GO:0006383 transcription from RNA polymerase III promoter IEA
BP GO:0006366 transcription from RNA polymerase II promoter IDA,TAS
BP GO:0006367 transcription initiation from RNA polymerase II promoter TAS
BP GO:0006361 transcription initiation from RNA polymerase I promoter TAS
BP GO:0016032 viral process IEA
CC GO:0005829 cytosol TAS
CC GO:0005736 DNA-directed RNA polymerase I complex IBA
CC GO:0005665 DNA-directed RNA polymerase II, core complex IDA
CC GO:0005666 DNA-directed RNA polymerase III complex IBA
CC GO:0005654 nucleoplasm IDA,TAS
CC GO:0005634 nucleus IDA,IEA
MF GO:0003677 DNA binding IEA
MF GO:0003899 DNA-directed RNA polymerase activity TAS,IEA
MF GO:0005515 protein binding IPI
MF GO:0001054 RNA polymerase I activity IBA
MF GO:0001055 RNA polymerase II activity IBA
MF GO:0001056 RNA polymerase III activity IBA

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
Cytosolic DNA-sensing pathway hsa04623
Epstein-Barr virus infection hsa05169
Huntington's disease hsa05016
Metabolic pathways hsa01100
Purine metabolism hsa00230
Pyrimidine metabolism hsa00240
RNA polymerase hsa03020