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

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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)

Download the association data used to generate this plot

 

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


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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