HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 357

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Apo B cis Discovery rs520354 2:21,259,612 A/G 0.47 996 0.303 0.042 6.9×10-13 1.110 6.6×10-13 2.5×10-12
Apo B cis Replication rs679899 2:21,250,914 A/G 0.47 337 -0.219 0.068 0.001 -1.110 0.001 0.006

 

Regional association plots

 

Boxplots and histograms for top associations

Apolipoprotein B (Apo B)

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

Apolipoprotein B (Apo B)

Target (abbrv.) Apo B
Target (full name) Apolipoprotein B
Somalogic ID (Sequence ID) SL000020 (2797-56_2)
Entrez Gene Symbol APOB
UniProt ID P04114
UniProt Comment
  • Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor.
Targeted by drugs (based on IPA annotation)
  • mipomersen
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
Wiki Pathways
  • Folate Metabolism
  • Selenium Pathway
  • Statin Pathway
  • Vitamin B12 Metabolism
Pathway Interaction Database
  • FOXA1 transcription factor network
  • amb2 Integrin signaling
Reactome
  • Cell surface interactions at the vascular wall
  • Chylomicron-mediated lipid transport
  • LDL-mediated lipid transport
  • Platelet sensitization by LDL
  • Retinoid metabolism and transport
  • Scavenging by Class A Receptors
  • Scavenging by Class B Receptors
  • Scavenging by Class F Receptors
  • Scavenging by Class H Receptors

All locus annotations are based on the sentinel SNP (rs520354) and 3 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

 

Results from other genome-wide association studies

Trait P Study Source
LDL cholesterol 4.4×10-52 24097068 (PMID) Supplemental file
Triglycerides 3.8×10-37 24097068 (PMID) Supplemental file
Total cholesterol 1.1×10-33 20686565 (PMID) GRASP2 nonQTL
HDL cholesterol 2.3×10-14 24097068 (PMID) Supplemental file
Serum ratio of (2-linoleoylglycerophosphoethanolamine*)/(creatine) 2.9×10-5 21886157 (PMID) GRASP2 metabQTL
Lipoproteins, ldl 9×10-5 pha002902 (dbGaP) dbGaP via SNiPA
Serum concentration of 1,7-dimethylurate 1.6×10-4 21886157 (PMID) GRASP2 metabQTL
Transmission distortion 3.9×10-4 22377632 (PMID) GRASP2 nonQTL