HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Home
Ideogram
Loci
Network view
Proteome annotation
Help
Locus annotations

Locus 170

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 rs2524280 6:31,416,990 C/A 0.07 995 -0.839 0.080 2.6×10-24 -1.810 3.3×10-25 1×10-11
MICA cis Replication rs12524487 6:31,354,238 G/A 0.06 337 -0.178 0.158 0.261 -1.120 0.205 0.218

 

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 (rs2524280) and 17 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
  • HCG27 HLA complex group 27 (non-protein coding)
  • PSORS1C3 psoriasis susceptibility 1 candidate 3 (non-protein coding)
  • ATP6V1G2-DDX39B ATP6V1G2-DDX39B readthrough (NMD candidate)
  • DDX39B DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
  • POU5F1 POU class 5 homeobox 1
  • Y_RNA
  • MICB MHC class I polypeptide-related sequence B
  • XXbac-BPG299F13.17
  • LY6G5C lymphocyte antigen 6 complex, locus G5C
  • HLA-C major histocompatibility complex, class I, C

 

Results from other genome-wide association studies

Trait P Study Source
Rheumatoid arthritis 7.6×10-30 20453842 (PMID) GRASP2 nonQTL
Rheumatoid arthritis (ACPA-positive) 5.6×10-21 21156761 (PMID) GRASP2 nonQTL
cg17169043 (chr6:170863821) 4.3×10-13 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Plasma Beta-2 microglobulin levels 1.5×10-12 23417110 (PMID) GRASP2 nonQTL
Beta-2 microglubulin plasma levels 2×10-12 23417110 (PMID) GWAS Catalog via SNiPA
Gene expression of MICA in liver 2.4×10-11 22006096 (PMID) GRASP2 eQTL
Gene expression of HLA-B in peripheral blood monocytes 8.4×10-11 20502693 (PMID) GRASP2 eQTL
Gene expression of AL645933.8 in blood 3.3×10-10 21829388 (PMID) GRASP2 eQTL
Gene expression of MICA (probeID ILMN_1655675) in whole blood 7.2×10-10 22692066 (PMID) GRASP2 eQTL
Gene expression of MICA (probeID ILMN_1797929) in cerebellum in Alzheimer's disease cases and controls 1.5×10-9 22685416 (PMID) GRASP2 eQTL
Ulcerative collitis 6.7×10-9 Supplemental file
Bipolar disorder, gender differentiated 8.5×10-9 17554300 (PMID) GRASP2 nonQTL
cg05496363 (chr11:66083790) 9.9×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Bipolar disorder 1×10-8 21254220 (PMID) GWAS Catalog via SNiPA
Gene expression of HLA-B in blood 1.2×10-8 21829388 (PMID) GRASP2 eQTL
cg01758672 (chr17:17743663) 3.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22213242 (chr11:66083549) 7.6×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg11067179 (chr11:66083565) 1.8×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of MICA (probeID ILMN_1797929) in cerebellum in Alzheimer's disease cases 3.2×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of DDAH2 in peripheral blood monocytes 9.7×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of LST1 in blood 1.8×10-6 21829388 (PMID) GRASP2 eQTL
Inflammatory bowel disease 1.8×10-6 Supplemental file
Gene expression of TIAM2 in peripheral blood monocytes 3.7×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of CARTPT in peripheral blood monocytes 4.1×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DQA1 in peripheral blood monocytes 6.5×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HCG27 in blood 6.4×10-5 21829388 (PMID) GRASP2 eQTL
Triglycerides 1.3×10-4 20686565 (PMID) GRASP2 nonQTL
Total cholesterol 2.1×10-4 24097068 (PMID) Supplemental file
Gene expression of MICA in CD4+ lymphocytes 3×10-4 20833654 (PMID) GRASP2 eQTL
Gene expression of [probe 1440603 centered at chr6:31556036] in blood 4.3×10-4 21829388 (PMID) GRASP2 eQTL