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

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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)

Download the association data used to generate this plot

 

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


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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