HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 175

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
MICA cis Discovery rs2516470 6:31,407,331 C/G 0.35 995 0.441 0.043 4.5×10-23 1.460 1×10-34 1.3×10-14

 

Regional association plots

MHC class I polypeptide-related sequence A (MICA)

 

Boxplots and histograms for top associations

MHC class I polypeptide-related sequence A (MICA)

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

MHC class I polypeptide-related sequence A (MICA)

Target (abbrv.) MICA
Target (full name) MHC class I polypeptide-related sequence A
Somalogic ID (Sequence ID) SL005199 (2730-58_2)
Entrez Gene Symbol MICA
UniProt ID Q29983
UniProt Comment
  • Seems to have no role in antigen presentation. Acts as a stress-induced self-antigen that is recognized by gamma delta T-cells. Ligand for the KLRK1/NKG2D receptor. Binding to KLRK1 leads to cell lysis.
Biomarker applications (based on IPA annotation)
  • safety
Pathway Studio
  • Natural Killer Cell Activation
  • Natural Killer Cell Activation through C-type Lectin-like Receptors

All locus annotations are based on the sentinel SNP (rs2516470).
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes

Genes hit or close-by
  • LINC01149 long intergenic non-protein coding RNA 1149
  • HCP5 HLA complex P5 (non-protein coding)
eQTL genes
  • ATP6V1G2 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2
  • HCG27 HLA complex group 27 (non-protein coding)
  • LST1 leukocyte specific transcript 1
  • LY6G5C lymphocyte antigen 6 complex, locus G5C
  • HCP5 HLA complex P5 (non-protein coding)
  • C4A complement component 4A (Rodgers blood group)
  • XXbac-BPG181B23.7
  • NOTCH4 notch 4
  • MICA MHC class I polypeptide-related sequence A
  • PRRC2A proline-rich coiled-coil 2A
  • HLA-B major histocompatibility complex, class I, B
  • XXbac-BPG248L24.12
  • MICB MHC class I polypeptide-related sequence B
  • HCG22 HLA complex group 22

 

Results from other genome-wide association studies

Trait P Study Source
Rheumatoid arthritis 8.4×10-11 20453842 (PMID) GRASP2 nonQTL
Gene expression of MICA (probeID ILMN_1797929) in cerebellum in Alzheimer's disease cases and controls 1.2×10-10 22685416 (PMID) GRASP2 eQTL
Gene expression of LOC282956 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 2.5×10-10 17873874 (PMID) GRASP2 eQTL
Height 5.2×10-10 25282103 (PMID) Supplemental file
Gene expression of MICA (probeID ILMN_1797929) in temporal cortex in Alzheimer's disease cases and controls 7.7×10-8 22685416 (PMID) GRASP2 eQTL