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WCMC

Connecting genetic risk to disease endpoints through the human blood plasma proteome

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Locus annotations

Locus 306

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
RUXF trans Discovery rs4420638 19:45,422,946 A/G 0.17 994 -0.435 0.056 3×10-14 -1.040 2.5×10-4 0.314
RUXF trans Replication rs4420638 19:45,422,946 A/G 0.12 337 -0.263 0.104 0.012 -1.050 0.031 0.126
Apo E2 cis Discovery rs4420638 19:45,422,946 A/G 0.17 994 0.419 0.056 1.9×10-13 1.070 1.9×10-12 1.5×10-13
Apo E2 cis Replication rs4420638 19:45,422,946 A/G 0.12 337 0.270 0.107 0.012 1.050 0.029 0.014

 

Regional association plots

Small nuclear ribonucleoprotein F (RUXF)

Download the association data used to generate this plot

Apolipoprotein E (isoform E2) (Apo E2)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Small nuclear ribonucleoprotein F (RUXF)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Apolipoprotein E (isoform E2) (Apo E2)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Small nuclear ribonucleoprotein F (RUXF)

Target (abbrv.) RUXF
Target (full name) Small nuclear ribonucleoprotein F
Somalogic ID (Sequence ID) SL009790 (5494-52_3)
Entrez Gene Symbol SNRPF
UniProt ID P62306
UniProt Comment
  • Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in an heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3'-end processing.
Wiki Pathways
  • mRNA processing
Reactome
  • Cleavage of Growing Transcript in the Termination Region
  • SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
  • SLBP independent Processing of Histone Pre-mRNAs
  • mRNA Splicing - Major Pathway
  • mRNA Splicing - Minor Pathway
  • snRNP Assembly

Apolipoprotein E (isoform E2) (Apo E2)

Target (abbrv.) Apo E2
Target (full name) Apolipoprotein E (isoform E2)
Somalogic ID (Sequence ID) SL000277 (5312-49_3)
Entrez Gene Symbol APOE
UniProt ID P02649
UniProt Comment
  • Mediates the binding, internalization, and catabolism of lipoprotein particles. It can serve as a ligand for the LDL (apo B/E) receptor and for the specific apo-E receptor (chylomicron remnant) of hepatic tissues.
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • prognosis
  • unspecified application
Wiki Pathways
  • Alzheimers Disease
  • Statin Pathway
  • Vitamin B12 Metabolism
Reactome
  • Chylomicron-mediated lipid transport
  • HDL-mediated lipid transport
  • Retinoid metabolism and transport
  • Scavenging by Class A Receptors

All locus annotations are based on the sentinel SNP (rs4420638) and 4 proxy variant(s) that is/are in linkage disequilibrium r2 ≥ 0.8. Linkage disequilibrium is based on data from the 1000 Genomes Project, phase 3 version 5, European population and was retrieved using SNiPA's Block Annotation feature.
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes

Genes hit or close-by