HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 271

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 rs4418214 6:31,391,401 T/C 0.06 979 -0.710 0.088 2.2×10-15 -1.630 3.7×10-15 3.7×10-8
MICA cis Replication rs4418214 6:31,391,401 A/G 0.06 337 -0.340 0.148 0.023 -1.190 0.032 0.127

 

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
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 (rs4418214) and 1 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
  • MICA MHC class I polypeptide-related sequence A
  • HCP5 HLA complex P5 (non-protein coding)
eQTL genes
  • MICA MHC class I polypeptide-related sequence A
  • XXbac-BPG181B23.7
  • MICB MHC class I polypeptide-related sequence B
  • TNXB tenascin XB
  • PSORS1C2 psoriasis susceptibility 1 candidate 2
  • TNXA tenascin XA (pseudogene)

 

Results from other genome-wide association studies

Trait P Study Source
HIV-1 control 1×10-34 21051598 (PMID) GWAS Catalog via SNiPA
HIV-1 control (elite control) 1.3×10-27 21051598 (PMID) GRASP2 nonQTL
Ankylosing spondylitis 2.3×10-24 22138694 (PMID) GRASP2 nonQTL
HIV-1 control (viral load at set point) 1.2×10-14 20041166 (PMID) GRASP2 nonQTL
HIV-1 susceptibility 4×10-11 23935489 (PMID) GWAS Catalog via SNiPA
Crohn's disease 1.1×10-8 Supplemental file
cg10154826 (chr6:17601018) 5.1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg02138124 (chr8:37901673) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Cross-disorder, subset Schizophrenia 1.7×10-4 23453885 (PMID) Supplemental file