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

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Locus annotations

Locus 263

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 rs28367631 6:31,267,936 C/T 0.35 995 -0.364 0.045 9.8×10-16 -1.250 7.5×10-13 1.5×10-7
MICA cis Replication rs4394275 6:31,318,177 G/A 0.22 337 -0.349 0.082 2.4×10-5 -1.220 1.5×10-5 0.019

 

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 (rs28367631) and 130 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
  • HCG27 HLA complex group 27 (non-protein coding)
  • PSORS1C2 psoriasis susceptibility 1 candidate 2
  • PSORS1C3 psoriasis susceptibility 1 candidate 3 (non-protein coding)
  • XXbac-BPG248L24.10
  • HLA-C major histocompatibility complex, class I, C
  • XXbac-BPG299F13.17
  • TCF19 transcription factor 19
  • WASF5P WAS protein family, member 5, pseudogene
  • HLA-B major histocompatibility complex, class I, B
  • CCHCR1 coiled-coil alpha-helical rod protein 1
  • XXbac-BPG248L24.12
  • HCG22 HLA complex group 22
  • POU5F1 POU class 5 homeobox 1
  • DDR1 discoidin domain receptor tyrosine kinase 1
  • MICB MHC class I polypeptide-related sequence B
  • PSORS1C1 psoriasis susceptibility 1 candidate 1
  • C4B complement component 4B (Chido blood group)
  • MICA MHC class I polypeptide-related sequence A
  • GPBAR1 G protein-coupled bile acid receptor 1
  • TMEM154 transmembrane protein 154
  • TRAPPC1 trafficking protein particle complex 1
  • CD248 CD248 molecule, endosialin
  • PLOD3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of HLA-C (probeID ILMN_1721113) in whole blood 3×10-41 22692066 (PMID) GRASP2 eQTL
Gene expression of HCG27 in blood 5.3×10-34 21829388 (PMID) GRASP2 eQTL
Gene expression of HLA-C in peripheral blood monocytes 4.1×10-28 20502693 (PMID) GRASP2 eQTL
Rheumatoid arthritis 1.1×10-17 20453842 (PMID) GRASP2 nonQTL
Total cholesterol 1.7×10-16 24097068 (PMID) Supplemental file
Height 1.9×10-16 25282103 (PMID) Supplemental file
HIV-1 control 3.7×10-16 21051598 (PMID) GRASP2 nonQTL
Gene expression of HLA-C (probeID ILMN_6270326) in whole blood 2.6×10-14 22692066 (PMID) GRASP2 eQTL
Gene expression of CCHCR1 [probe 42361_g_at] in lymphoblastoid cell lines 1.2×10-13 17873877 (PMID) GRASP2 eQTL
Gene expression of CCHCR1 in lymphoblastoid cell lines 2.9×10-12 17873877 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in Alzheimer's disease cases and controls 3.4×10-12 22685416 (PMID) GRASP2 eQTL
Population differentiation markers among Great Britain 1.1×10-11 17554300 (PMID) GRASP2 nonQTL
Gene expression of TMEM154 in blood 1.1×10-10 21829388 (PMID) GRASP2 eQTL
Gene expression of PLOD3 in blood 2.2×10-10 21829388 (PMID) GRASP2 eQTL
Gene expression of CCHCR1 [probe 37424_at] in lymphoblastoid cell lines 3.3×10-10 17873877 (PMID) GRASP2 eQTL
Gene expression of VARS2 in peripheral blood monocytes 9.2×10-10 20502693 (PMID) GRASP2 eQTL
Gene expression of CCHCR1 [probe 209698_at] in lymphoblastoid cell lines 2.3×10-9 17873877 (PMID) GRASP2 eQTL
Triglycerides 4.8×10-9 20686565 (PMID) GRASP2 nonQTL
Gene expression of CCHCR1 [probe 37425_g_at] in lymphoblastoid cell lines 7×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in temporal cortex in Alzheimer's disease cases and controls 1.4×10-8 22685416 (PMID) GRASP2 eQTL
Gene expression of MICA in peripheral blood monocytes 1.6×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-B in peripheral blood monocytes 2.1×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of HCG27 (probeID ILMN_1746436) in temporal cortex in Alzheimer's disease cases and controls 2.2×10-8 22685416 (PMID) GRASP2 eQTL
Gene expression of TCF19 [probe 223274_at] in lymphoblastoid cell lines 3.2×10-8 17873877 (PMID) GRASP2 eQTL
Gene expression of BTN3A2 in peripheral blood monocytes 4.9×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in non-Alzheimer's disease samples 2.3×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of TCF19 in lymphoblastoid cell lines 2.3×10-7 17873877 (PMID) GRASP2 eQTL
Gene expression of EVC in peripheral blood monocytes 8.2×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of NCOA1 in peripheral blood monocytes 9.9×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DQA1 in peripheral blood monocytes 1.3×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HCG27 (probeID ILMN_1746436) in temporal cortex in Alzheimer's disease cases 1.7×10-6 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in Alzheimer's disease cases 2.8×10-6 22685416 (PMID) GRASP2 eQTL
Protein quantitative trait loci 4×10-6 18464913 (PMID) GWAS Catalog via SNiPA
IL18 4×10-6 18464913 (PMID) GRASP2 nonQTL
Differential exon level expression of HLA-C [probe 2948915] in peripheral blood mononuclear cells 4.1×10-6 19222302 (PMID) GRASP2 eQTL
Gene expression of HLA-B in blood 6.1×10-6 21829388 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in temporal cortex in non-Alzheimer's disease samples 9.8×10-6 22685416 (PMID) GRASP2 eQTL
Gene expression of PSORS1C3 in normal prepouch ileum 2×10-5 23474282 (PMID) GRASP2 eQTL
Psoriatic arthritis 4.9×10-5 18369459 (PMID) GRASP2 nonQTL
HIV-1 disease progression 1×10-4 20041166 (PMID) GRASP2 nonQTL
Schizophrenia 1.9×10-4 25056061 (PMID) Supplemental file
Plasma brain natriuretic peptide (BNP) 2.3×10-4 20877124 (PMID) GRASP2 nonQTL
Type 2 diabetes 3×10-4 22885922 (PMID) Supplemental file
Type 1 diabetes, combined control dataset 4×10-4 17554300 (PMID) GRASP2 nonQTL