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

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Locus annotations

Locus 10

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
FCG2A/B cis Discovery rs17413015 1:161,644,811 C/T 0.15 987 1.361 0.046 9.2×10-137 2.390 2.3×10-150 1×10-186
FCG2A/B cis Replication rs12118043 1:161,646,824 C/A 0.11 337 1.515 0.086 1.5×10-49 2.620 9.1×10-66 1.3×10-81

 

Regional association plots

Low affinity immunoglobulin gamma Fc region receptor II-a/b (FCG2A/B)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Low affinity immunoglobulin gamma Fc region receptor II-a/b (FCG2A/B)

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

Low affinity immunoglobulin gamma Fc region receptor II-a/b (FCG2A/B)

Target (abbrv.) FCG2A/B
Target (full name) Low affinity immunoglobulin gamma Fc region receptor II-a/b
Somalogic ID (Sequence ID) SL017613 (3310-62_1)
Entrez Gene Symbol FCGR2A
UniProt ID P12318, P31994
UniProt Comment
  • P12318: Binds to the Fc region of immunoglobulins gamma. Low affinity receptor. By binding to IgG it initiates cellular responses against pathogens and soluble antigens. Promotes phagocytosis of opsonized antigens.
  • P31994: Receptor for the Fc region of complexed or aggregated immunoglobulins gamma. Low affinity receptor. Involved in a variety of effector and regulatory functions such as phagocytosis of immune complexes and modulation of antibody production by B-cells. Binding to this receptor results in down-modulation of previous state of cell activation triggered via antigen receptors on B-cells (BCR), T-cells (TCR) or via another Fc receptor. Isoform IIB1 fails to mediate endocytosis or phagocytosis. Isoform IIB2 does not trigger phagocytosis.
Pathway Interaction Database
  • BCR signaling pathway
  • Fc-epsilon receptor I signaling in mast cells
Reactome
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Pathway Studio
  • T-cell-Independent B-cell Activation

All locus annotations are based on the sentinel SNP (rs17413015) 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


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Genes hit or close-by
eQTL genes
  • FCGR2C Fc fragment of IgG, low affinity IIc, receptor for (CD32) (gene/pseudogene)
  • FCGR3B Fc fragment of IgG, low affinity IIIb, receptor (CD16b)
  • FCRLB Fc receptor-like B
  • FCGR2B Fc fragment of IgG, low affinity IIb, receptor (CD32)

 

Results from other genome-wide association studies

Trait P Study Source
P31994 protein abundance levels 1.3×10-11 22595970 (PMID) GRASP2 pQTL
Gene expression of USF1 in liver 2.7×10-5 18462017 (PMID) GRASP2 eQTL
Birth weight 9.9×10-5 23202124 (PMID) Supplemental file
Serum ratio of (gamma-glutamylisoleucine*)/(theobromine) 3.1×10-4 21886157 (PMID) GRASP2 metabQTL

FCGR2B protein levels may influence the risk to develop auto-immune disorders.

Two replicated cis-pQTLs with Low affinity immunoglobulin gamma Fc region receptor II-b (FCGR2B). rs7551957 is a strong GWAS hit for Inflammatory bowel disease (p<2×10-38) and related auto-immune diseases (Ulcerative colitis, Kawasaki disease, systemic lupus erythematous, Inflammatory bowel disease). This association can shed new light on the functional background of the role of FCGR2B in Chrohn's disease. See also Locus 141 for an association with the ratio of FCGR2B and FCGR3B.

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.