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WCMC

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

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Locus annotations

Locus 332

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
NKG2D cis Discovery rs2255336 12:10,532,326 C/T 0.22 996 0.399 0.053 1.3×10-13 1.060 0.005 0.785
NKG2D cis Replication rs2255336 12:10,532,326 G/A 0.17 337 0.194 0.091 0.034 1.050 0.17 0.385

 

Regional association plots

NKG2-D type II integral membrane protein (NKG2D)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

NKG2-D type II integral membrane protein (NKG2D)

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

NKG2-D type II integral membrane protein (NKG2D)

Target (abbrv.) NKG2D
Target (full name) NKG2-D type II integral membrane protein
Somalogic ID (Sequence ID) SL005204 (3056-11_1)
Entrez Gene Symbol KLRK1
UniProt ID P26718
UniProt Comment
  • Function as an activating and costimulatory receptor involved in immunosurveillance upon binding to various cellular stress-inducible ligands displayed at the surface of autologous tumor cells and virus-infected cells. Provides both stimulatory and costimulatory innate immune responses on activated killer (NK) cells, leading to cytotoxic activity. Acts as a costimulatory receptor for T-cell receptor (TCR) in CD8(+) T-cell-mediated adaptive immune responses by amplifying T-cell activation. Stimulates perforin-mediated elimination of ligand-expressing tumor cells. Signaling involves calcium influx, culminating in the expression of TNF-alpha. Participates in NK cell-mediated bone marrow graft rejection. May play a regulatory role in differentiation and survival of NK cells. Binds to ligands belonging to various subfamilies of MHC class I-related glycoproteins including MICA, MICB, RAET1E, RAET1G, ULBP1, ULBP2, ULBP3 (ULBP2>ULBP1>ULBP3) and ULBP4.
Reactome
  • DAP12 interactions
  • DAP12 signaling
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

All locus annotations are based on the sentinel SNP (rs2255336) and 73 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
  • RP11-277P12.9
  • RP11-277P12.20
  • KLRK1 killer cell lectin-like receptor subfamily K, member 1
  • KLRC4-KLRK1 KLRC4-KLRK1 readthrough
  • KLRC4 killer cell lectin-like receptor subfamily C, member 4
  • KLRC3 killer cell lectin-like receptor subfamily C, member 3
  • RP11-277P12.6
  • KLRC2 killer cell lectin-like receptor subfamily C, member 2
  • KLRC1 killer cell lectin-like receptor subfamily C, member 1
Potentially regulated genes
  • CLEC1A C-type lectin domain family 1, member A
  • KLRC2 killer cell lectin-like receptor subfamily C, member 2
  • KLRK1 killer cell lectin-like receptor subfamily K, member 1
  • KLRC3 killer cell lectin-like receptor subfamily C, member 3
  • KLRD1 killer cell lectin-like receptor subfamily D, member 1
eQTL genes
  • GABARAPL1 GABA(A) receptor-associated protein like 1
  • KLRK1 killer cell lectin-like receptor subfamily K, member 1
  • KLRC2 killer cell lectin-like receptor subfamily C, member 2
  • KLRD1 killer cell lectin-like receptor subfamily D, member 1
  • RP11-277P12.10
  • RP11-277P12.20
  • KLRC4-KLRK1 KLRC4-KLRK1 readthrough
  • KLRC3 killer cell lectin-like receptor subfamily C, member 3
  • YBX3 Y box binding protein 3
  • KLRC1 killer cell lectin-like receptor subfamily C, member 1
  • TAS2R10 taste receptor, type 2, member 10

 

Results from other genome-wide association studies

Trait P Study Source
"Gene expression of KLRC2 [transcript NM_002260, probe A_23_P22232] in liver" 9.2×10-13 21637794 (PMID) GRASP2 eQTL
Gene expression of KLRK1 [probe 205821_at] in lymphoblastoid cell lines 1.9×10-12 17873877 (PMID) GRASP2 eQTL
Gene expression of CSDA in peripheral blood monocytes 1.1×10-11 20502693 (PMID) GRASP2 eQTL
Gene expression of KLRK1 [probe ILMN_2059357] in peripheral leukocytes 2.3×10-10 19966804 (PMID) GRASP2 eQTL
Methylation levels at chr12:10479433-10479483 [hg18 coord, probe cg22432908] in Frontal cortex 2.3×10-10 20485568 (PMID) GRASP2 meQTL
Gene expression of KLRC4 [probe 1555691_a_at] in lymphoblastoid cell lines 1×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of KLRK1 [probe 1555691_a_at] in lymphoblastoid cell lines 1×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of KLRK1 in CEU-CHB-JPT lymphoblastoid cell lines 6.6×10-9 17873874 (PMID) GRASP2 eQTL
Differential exon level expression of KLRC3 [probe 3444136] in brain cortex 3.3×10-7 19222302 (PMID) GRASP2 eQTL
Gene expression of KLRC3 in blood 2.2×10-6 21829388 (PMID) GRASP2 eQTL
Obesity-related traits 6×10-6 23251661 (PMID) GWAS Catalog via SNiPA
Maximum oxygen consumption during treadmill fitness test (VO2max) (mL/min) in children 6.2×10-6 23251661 (PMID) GRASP2 nonQTL
Gene expression of KLRC2 in normal prepouch ileum 8.9×10-6 23474282 (PMID) GRASP2 eQTL
Behet's disease 1.2×10-5 20622879 (PMID) GRASP2 nonQTL
Gene expression of KLRC2 in blood 3.1×10-5 21829388 (PMID) GRASP2 eQTL
Differential exon level expression of KLRC1 [probe 3444149] in brain cortex 4.1×10-5 19222302 (PMID) GRASP2 eQTL
Gene expression of KLRK1 in blood 7.3×10-5 21829388 (PMID) GRASP2 eQTL
Gene expression of KLRC4 in normal prepouch ileum 8.6×10-5 23474282 (PMID) GRASP2 eQTL
Primary rhegmatogenous retinal detachment 4.4×10-4 23585552 (PMID) GRASP2 nonQTL