HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Home
Ideogram
Loci
Network view
Proteome annotation
Help
Locus annotations

Locus 141

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
FCG3B cis Discovery rs10919544 1:161,508,763 T/C 0.38 992 0.477 0.042 3.5×10-28 1.140 2.2×10-27 7.7×10-23
FCG3B cis Replication rs10919544 1:161,508,763 A/G 0.37 337 0.492 0.065 5.9×10-13 1.160 1.2×10-11 3.3×10-7
FCG2A/B cis Discovery rs10919544 1:161,508,763 T/C 0.38 992 -0.414 0.043 6.4×10-21 -1.300 1.2×10-21 1.6×10-21
FCG2A/B cis Replication rs10919544 1:161,508,763 A/G 0.37 337 -0.197 0.073 0.007 -1.140 0.001 0.001

 

Regional association plots

Low affinity immunoglobulin gamma Fc region receptor III-B (FCG3B)

Download the association data used to generate this plot

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 III-B (FCG3B)

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)

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

Low affinity immunoglobulin gamma Fc region receptor III-B (FCG3B)

Target (abbrv.) FCG3B
Target (full name) Low affinity immunoglobulin gamma Fc region receptor III-B
Somalogic ID (Sequence ID) SL008609 (3311-27_1)
Entrez Gene Symbol FCGR3B
UniProt ID O75015
UniProt Comment
  • Receptor for the Fc region of immunoglobulins gamma. Low affinity receptor. Binds complexed or aggregated IgG and also monomeric IgG. Contrary to III-A, is not capable to mediate antibody-dependent cytotoxicity and phagocytosis. May serve as a trap for immune complexes in the peripheral circulation which does not activate neutrophils.
Targeted by drugs (based on IPA annotation)
  • IgG
Pathway Studio
  • Natural Killer Cell Activation through ITAM-Containing Receptors

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 (rs10919544) 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

Genes hit or close-by
  • RP11-25K21.6
  • HSPA6 heat shock 70kDa protein 6 (HSP70B')
  • RPS23P10 ribosomal protein S23 pseudogene 10
  • FCGR3A Fc fragment of IgG, low affinity IIIa, receptor (CD16a)
Potentially regulated genes
  • USF1 upstream transcription factor 1
  • UFC1 ubiquitin-fold modifier conjugating enzyme 1
  • TOMM40L translocase of outer mitochondrial membrane 40 homolog (yeast)-like
  • HSPA6 heat shock 70kDa protein 6 (HSP70B')
eQTL genes
  • FCRLB Fc receptor-like B
  • RPS23P10 ribosomal protein S23 pseudogene 10
  • RPS23P9 ribosomal protein S23 pseudogene 9
  • FCGR2C Fc fragment of IgG, low affinity IIc, receptor for (CD32) (gene/pseudogene)
  • FCGR2B Fc fragment of IgG, low affinity IIb, receptor (CD32)
  • HSPA7 heat shock 70kDa protein 7 (HSP70B)

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of HSPA6 in blood 2.3×10-32 21829388 (PMID) GRASP2 eQTL
Gene expression of HSPA6///AL451067.12 in blood 4.3×10-32 21829388 (PMID) GRASP2 eQTL
Methylation levels at chr1:159785970-159786020 [hg18 coord, probe cg04384208] in Cerebellum 5.8×10-12 20485568 (PMID) GRASP2 meQTL
Methylation levels at chr1:159785970-159786020 [hg18 coord, probe cg04384208] in Temporal cortex 1×10-10 20485568 (PMID) GRASP2 meQTL
"Gene expression of FCGR2A [transcript NM_021642, probe A_32_P74942] in liver" 1.2×10-10 21637794 (PMID) GRASP2 eQTL
Methylation levels at chr1:159785970-159786020 [hg18 coord, probe cg04384208] in Frontal cortex 4.2×10-9 20485568 (PMID) GRASP2 meQTL
Serum ratio of (hyodeoxycholate)/(theophylline) 5.5×10-6 21886157 (PMID) GRASP2 metabQTL
Ulcerative collitis 6.8×10-5 Supplemental file

Ratio between protein concentrations; anti-correlation.

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.