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

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Locus annotations

Locus 174

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
NKp30 cis Discovery rs6916921 6:31,520,426 C/T 0.13 996 -0.619 0.061 2.2×10-23 -1.080 1.7×10-8 0.053
NKp30 cis Replication rs6916921 6:31,520,426 G/A 0.12 337 -0.693 0.091 3.7×10-13 -1.090 0.004 0.234

 

Regional association plots

Natural cytotoxicity triggering receptor 3 (NKp30)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Natural cytotoxicity triggering receptor 3 (NKp30)

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

Natural cytotoxicity triggering receptor 3 (NKp30)

Target (abbrv.) NKp30
Target (full name) Natural cytotoxicity triggering receptor 3
Somalogic ID (Sequence ID) SL005205 (3003-29_2)
Entrez Gene Symbol NCR3
UniProt ID O14931
UniProt Comment
  • Cytotoxicity-activating receptor that contributes to the increased efficiency of activated natural killer (NK) cells to mediate tumor cell lysis. Engagement of NCR3 by BAG6 also promotes dendritic cell (DC) maturation, both through killing those DCs that did not properly acquire a mature phenotype, and inducing NK cells to release TNFA and IFNG, which promotes DC maturation.
Pathway Studio
  • Natural Killer Cell Activation
  • Natural Killer Cell Activation through ITAM-Containing Receptors

All locus annotations are based on the sentinel SNP (rs6916921) 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
  • ATP6V1G2 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2
  • NFKBIL1 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1
  • TNF tumor necrosis factor
  • LTA lymphotoxin alpha
  • LTB lymphotoxin beta (TNF superfamily, member 3)
  • LST1 leukocyte specific transcript 1
  • NCR3 natural cytotoxicity triggering receptor 3
Potentially regulated genes
eQTL genes
  • ATP6V1G2 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2
  • LST1 leukocyte specific transcript 1
  • XXbac-BPG181B23.7
  • XXbac-BPG299F13.17
  • AIF1 allograft inflammatory factor 1
  • MICA MHC class I polypeptide-related sequence A
  • BAG6 BCL2-associated athanogene 6
  • MICB MHC class I polypeptide-related sequence B
  • PSORS1C1 psoriasis susceptibility 1 candidate 1
  • NCR3 natural cytotoxicity triggering receptor 3
  • HLA-B major histocompatibility complex, class I, B

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of NCR3 in CD4+ lymphocytes 3.2×10-22 20833654 (PMID) GRASP2 eQTL
Gene expression of LST1///NCR3 in blood 8.2×10-22 21829388 (PMID) GRASP2 eQTL
Gene expression of LST1 in blood 2.6×10-18 21829388 (PMID) GRASP2 eQTL
Gene expression of ATP6V1G2 [probe ILMN_18630] in osteoblasts 2.9×10-10 19654370 (PMID) GRASP2 eQTL
Gene expression of AIF1 in blood 7.1×10-10 21829388 (PMID) GRASP2 eQTL
Grave's disease 8×10-8 21900946 (PMID) GRASP2 nonQTL
Differential exon level expression of NCR3 [probe 2949137] in peripheral blood mononuclear cells 1.4×10-7 19222302 (PMID) GRASP2 eQTL
Gene expression of LTA in blood 4.3×10-5 21829388 (PMID) GRASP2 eQTL
Inflammatory bowel disease 5.4×10-5 Supplemental file
Gene expression of ATP6V1G2 in CD4+ lymphocytes 1.3×10-4 20833654 (PMID) GRASP2 eQTL
Gene expression of ATP6V1G2///BAT1 in blood 1.3×10-4 21829388 (PMID) GRASP2 eQTL
Gene expression of BAT3 in blood 1.5×10-4 21829388 (PMID) GRASP2 eQTL
Ulcerative collitis 2.9×10-4 Supplemental file
Rheumatoid arthritis 3.4×10-4 19503088 (PMID) GRASP2 nonQTL
Height 4.4×10-4 25282103 (PMID) Supplemental file