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

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Locus annotations

Locus 63

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
SLAF7 cis Discovery rs489286 1:160,722,550 G/A 0.35 996 -0.691 0.040 1.5×10-57 -1.510 1.2×10-62 4.7×10-40
SLAF7 cis Replication rs518721 1:160,723,517 G/A 0.29 337 -0.359 0.069 3.2×10-7 -1.300 1.7×10-10 6.5×10-6

 

Regional association plots

 

Boxplots and histograms for top associations

SLAM family member 7 (SLAF7)

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

SLAM family member 7 (SLAF7)

Target (abbrv.) SLAF7
Target (full name) SLAM family member 7
Somalogic ID (Sequence ID) SL016928 (5487-7_3)
Entrez Gene Symbol SLAMF7
UniProt ID Q9NQ25
UniProt Comment
  • Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Isoform 1 mediates NK cell activation through a SH2D1A-independent extracellular signal-regulated ERK-mediated pathway (PubMed:11698418). Positively regulates NK cell functions by a mechanism dependent on phosphorylated SH2D1B. Downstream signaling implicates PLCG1, PLCG2 and PI3K (PubMed:16339536). In addition to heterotypic NK cells-target cells interactions also homotypic interactions between NK cells may contribute to activation. However, in the absence of SH2D1B, inhibits NK cell function. Acts also inhibitory in T-cells (By similarity). May play a role in lymphocyte adhesion (PubMed:11802771). In LPS-activated monocytes negatively regulates production of proinflammatory cytokines (PubMed:23695528).
Pathway Studio
  • Natural Killer Cell Activation through ITSM-Containing Receptors

All locus annotations are based on the sentinel SNP (rs489286) and 12 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
Potentially regulated genes
  • SLAMF1 signaling lymphocytic activation molecule family member 1
  • B4GALT3 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3
  • NCSTN nicastrin
  • LY9 lymphocyte antigen 9
  • PVRL4 poliovirus receptor-related 4
  • RP11-544M22.3
eQTL genes
  • SLAMF7 SLAM family member 7
  • LY9 lymphocyte antigen 9

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of SLAMF7 [probe 222838_at] in lymphoblastoid cell lines 2.7×10-11 17873877 (PMID) GRASP2 eQTL
cg04244970 (chr1:160708963) 4.5×10-10 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of LY9 in blood 5.2×10-9 21829388 (PMID) GRASP2 eQTL
Gene expression of SLAMF7 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 1.1×10-8 17873874 (PMID) GRASP2 eQTL
Gene expression of LY9 [probe 231124_x_at] in lymphoblastoid cell lines 9×10-8 17873877 (PMID) GRASP2 eQTL
Serum ratio of (alpha-ketoglutarate)/(paraxanthine) 6.2×10-5 21886157 (PMID) GRASP2 metabQTL
Serum ratio of (3-methyl-2-oxobutyrate)/(3-methyl-2-oxovalerate) 2.1×10-4 21886157 (PMID) GRASP2 metabQTL
Serum concentration of asparagine 4.7×10-4 21886157 (PMID) GRASP2 metabQTL

Genetic variant in a cancer target.

This locus is discussed in the main paper.

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.