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

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Locus annotations

Locus 167

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 rs9469012 6:31,421,300 G/A 0.12 991 -0.694 0.066 9.6×10-25 -1.650 9.6×10-27 5.4×10-11
MICA cis Replication rs10223568 6:31,390,203 A/G 0.24 337 -0.627 0.072 1.7×10-16 -1.410 1.5×10-16 3.6×10-6

 

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
Replication 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 (rs9469012) and 21 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
Potentially regulated genes
eQTL genes
  • MICA MHC class I polypeptide-related sequence A
  • HLA-B major histocompatibility complex, class I, B
  • XXbac-BPG181B23.7
  • HCG22 HLA complex group 22
  • LY6G5C lymphocyte antigen 6 complex, locus G5C

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of LOC282956 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 8.6×10-20 17873874 (PMID) GRASP2 eQTL
Height 2×10-15 25282103 (PMID) Supplemental file
HIV-1 control 7.5×10-10 21051598 (PMID) GRASP2 nonQTL
Triglycerides 5.8×10-9 24097068 (PMID) Supplemental file
Gene expression of MICA in normal prepouch ileum 8.9×10-9 23474282 (PMID) GRASP2 eQTL
LDL cholesterol 8.3×10-8 24097068 (PMID) Supplemental file
Gene expression of HCG4 in peripheral blood monocytes 1.2×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of LOC282956 in YRI lymphoblastoid cell lines 2.5×10-7 17873874 (PMID) GRASP2 eQTL
Behcet syndrome 1.3×10-6 pha002888 (dbGaP) dbGaP via SNiPA
Total cholesterol 5.5×10-6 20686565 (PMID) GRASP2 nonQTL
Rate of HIV-1 progression to clinical AIDS 1.3×10-5 20064070 (PMID) GRASP2 nonQTL
LDL cholesterol change with statins 2.5×10-5 20339536 (PMID) GRASP2 nonQTL
Total cholesterol change with statins 5.3×10-5 20339536 (PMID) GRASP2 nonQTL
Rheumatoid arthritis 1.4×10-4 20453842 (PMID) GRASP2 nonQTL
Cervical cancer 4.7×10-4 21716314 (PMID) GRASP2 nonQTL