HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 315

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
IGF-II receptor cis Discovery rs9295123 6:160,570,114 G/A 0.42 993 0.331 0.043 5.3×10-14 1.060 9.2×10-14 2.5×10-13
IGF-II receptor cis Replication rs13212914 6:160,570,624 G/A 0.41 337 0.294 0.065 8.7×10-6 1.070 7.2×10-6 2.7×10-5

 

Regional association plots

Cation-independent mannose-6-phosphate receptor (IGF-II receptor)

 

Boxplots and histograms for top associations

Cation-independent mannose-6-phosphate receptor (IGF-II receptor)

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

Cation-independent mannose-6-phosphate receptor (IGF-II receptor)

Target (abbrv.) IGF-II receptor
Target (full name) Cation-independent mannose-6-phosphate receptor
Somalogic ID (Sequence ID) SL003679 (3676-15_3)
Entrez Gene Symbol IGF2R
UniProt ID P11717
UniProt Comment
  • Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6-phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex. This receptor also binds IGF2. Acts as a positive regulator of T-cell coactivation, by binding DPP4.
Wiki Pathways
  • Adipocyte TarBase
  • Epithelium TarBase
  • Leukocyte TarBase
  • Lymphocyte TarBase
  • Muscle cell TarBase
Reactome
  • Golgi Associated Vesicle Biogenesis
Pathway Studio
  • Golgi to Endosome Transport
  • Transcytosis

All locus annotations are based on the sentinel SNP (rs9295123) and 13 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
  • SLC22A1 solute carrier family 22 (organic cation transporter), member 1
eQTL genes
  • SLC22A1 solute carrier family 22 (organic cation transporter), member 1
  • MAS1 MAS1 proto-oncogene, G protein-coupled receptor

 

Results from other genome-wide association studies

Trait P Study Source
LDL cholesterol 1.3×10-15 24097068 (PMID) Supplemental file
Triglycerides 3.3×10-15 24097068 (PMID) Supplemental file
isobutyrylcarnitine 2.4×10-14 24816252 (PMID) gwas.eu via SNiPA
Coronary artery disease (CAD) 3.2×10-7 22319020 (PMID) GRASP2 nonQTL
Total cholesterol 1.2×10-6 20686565 (PMID) GRASP2 nonQTL
Prostate cancer 2.1×10-5 20676098 (PMID) GRASP2 nonQTL
HIV-1 control (viral load) 2.2×10-5 21490045 (PMID) GRASP2 nonQTL
Differential exon level expression of IGF2R [probe 2934428] in brain cortex 6.5×10-5 19222302 (PMID) GRASP2 eQTL
Lipoproteins 7.1×10-5 pha003079 (dbGaP) dbGaP via SNiPA