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


Proteome annotation
Locus annotations

Locus 196

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
LY9 cis Discovery rs540254 1:160,767,737 T/C 0.35 995 0.417 0.045 7.8×10-20 1.120 2.2×10-18 1.1×10-15


Regional association plots

T-lymphocyte surface antigen Ly-9 (LY9)


Boxplots and histograms for top associations

T-lymphocyte surface antigen Ly-9 (LY9)

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

T-lymphocyte surface antigen Ly-9 (LY9)

Target (abbrv.) LY9
Target (full name) T-lymphocyte surface antigen Ly-9
Somalogic ID (Sequence ID) SL007674 (3324-51_1)
Entrez Gene Symbol LY9
UniProt ID Q9HBG7
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. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).

All locus annotations are based on the sentinel SNP (rs540254) and 6 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
  • LY9 lymphocyte antigen 9
eQTL genes
  • SLAMF7 SLAM family member 7
  • LY9 lymphocyte antigen 9


Results from other genome-wide association studies

Trait P Study Source
cg18865207 (chr1:160765895) 2.1×10-32 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of LY9 in blood 1.1×10-22 21829388 (PMID) GRASP2 eQTL
Serum ratio of (decanoylcarnitine)/(succinylcarnitine) 6.6×10-6 21886157 (PMID) GRASP2 metabQTL
Serum concentration of 1-oleoylglycerol (1-monoolein) 2.6×10-5 21886157 (PMID) GRASP2 metabQTL