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WCMC

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

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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


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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