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WCMC

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

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Locus annotations

Locus 358

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 rs12202350 6:160,379,096 T/C 0.11 995 0.510 0.070 7.1×10-13 1.090 9.3×10-13 2×10-14

 

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

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 (rs12202350) and 7 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
  • MAS1 MAS1 proto-oncogene, G protein-coupled receptor
  • IGF2R insulin-like growth factor 2 receptor
Potentially regulated genes
  • TCP1 t-complex 1
  • SOD2 superoxide dismutase 2, mitochondrial
eQTL genes
  • RP11-288H12.3
  • SLC22A1 solute carrier family 22 (organic cation transporter), member 1
  • IGF2R insulin-like growth factor 2 receptor
  • WTAP Wilms tumor 1 associated protein

 

Results from other genome-wide association studies

Trait P Study Source
isobutyrylcarnitine 5.1×10-18 24816252 (PMID) gwas.eu via SNiPA
Triglycerides 4.3×10-7 24097068 (PMID) Supplemental file
LDL cholesterol 2.4×10-6 24097068 (PMID) Supplemental file
cg06131755 (chr6:160182471) 4.2×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
T2 lesion load (multiple sclerosis) 7.9×10-6 19010793 (PMID) GRASP2 nonQTL
Lesion load (multiple sclerosis) 7.9×10-6 19010793 (PMID) GRASP2 nonQTL
cg05504194 (chr6:160182648) 1.8×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25736982 (chr6:160182578) 2.1×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs