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WCMC

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

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Locus annotations

Locus 13

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 rs2844511 6:31,389,784 G/A 0.40 995 0.922 0.034 3.8×10-119 1.860 2.8×10-109 7.7×10-51
MICA cis Replication rs2596530 6:31,387,373 A/G 0.16 337 0.616 0.089 2.7×10-11 1.370 7.9×10-10 1.7×10-4

 

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 (rs2844511) and 9 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)
Potentially regulated genes
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression 2×10-62 20881960 (PMID) GRASP2 nonQTL
cg23656755 (chr1:230203067) 2.6×10-41 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06606381 (chr12:133084921) 1.2×10-39 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg01620082 (chr3:125678431) 2×10-39 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17862947 (chr12:133086950) 6.5×10-38 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Height 2.5×10-36 25282103 (PMID) Supplemental file
Gene expression of MICA (probeID ILMN_1797929) in temporal cortex in Alzheimer's disease cases and controls 2.2×10-27 22685416 (PMID) GRASP2 eQTL
Gene expression of XRCC6 in blood 4.2×10-24 21829388 (PMID) GRASP2 eQTL
cg17169043 (chr6:170863821) 4×10-20 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HCG27 in blood 9×10-19 21829388 (PMID) GRASP2 eQTL
Cervical cancer 1.6×10-18 23482656 (PMID) GRASP2 nonQTL
CERVICAL CANCER 4×10-18 23482656 (PMID) GWAS Catalog via SNiPA
Gene expression of MICA in normal prepouch ileum 1.3×10-17 23474282 (PMID) GRASP2 eQTL
Gene expression of TMEM154 in blood 3.7×10-17 21829388 (PMID) GRASP2 eQTL
Gene expression of MICA (probeID ILMN_1797929) in temporal cortex in non-Alzheimer's disease samples 1.4×10-16 22685416 (PMID) GRASP2 eQTL
cg02753903 (chr19:38943549) 1.5×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Idiopathic membranous nephropathy 1.9×10-14 21323541 (PMID) GRASP2 nonQTL
cg22379212 (chr19:38944024) 5.7×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of MICA (probeID ILMN_1797929) in temporal cortex in Alzheimer's disease cases 1.1×10-11 22685416 (PMID) GRASP2 eQTL
Gene expression of LOC282956 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 1.2×10-11 17873874 (PMID) GRASP2 eQTL
Triglycerides 2.7×10-11 24097068 (PMID) Supplemental file
cg01255021 (chr16:1094629) 4.5×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Rheumatoid arthritis 1.1×10-10 20453842 (PMID) GRASP2 nonQTL
HIV-1 control (viral load at set point) 1.1×10-10 20041166 (PMID) GRASP2 nonQTL
Gene expression of LOC285835 [probe 230937_at] in lymphoblastoid cell lines 1.1×10-10 17873877 (PMID) GRASP2 eQTL
cg04788957 (chr10:105438032) 1.3×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HIV-1 control 2.1×10-9 21051598 (PMID) GRASP2 nonQTL
Lupus erythematosus, systemic 3.6×10-9 pha002848 (dbGaP) dbGaP via SNiPA
cg10154826 (chr6:17601018) 3.7×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg09408951 (chr1:187673755) 6.2×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg25652859 (chr20:57427388) 1.2×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of LST1///NCR3 in blood 1.2×10-8 21829388 (PMID) GRASP2 eQTL
cg20954971 (chr21:44593666) 1.3×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg27443779 (chr11:14664769) 1.4×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19313311 (chr7:74058055) 1.4×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19589727 (chr20:57427786) 1.6×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Height (adults) 3.2×10-8 21194676 (PMID) GRASP2 nonQTL
Behcet syndrome 4.3×10-8 pha002888 (dbGaP) dbGaP via SNiPA
cg14564778 (chr20:57427532) 5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg03059896 (chr1:27560026) 8.9×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17841099 (chr1:153940066) 9×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06065549 (chr20:57427419) 1.3×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg00943909 (chr20:57427966) 1.3×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Total cholesterol 1.5×10-7 23063622 (PMID) GRASP2 nonQTL
cg14153654 (chr1:8001003) 2×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg05496363 (chr11:66083790) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HIV-1 seropositive nonprogression 4.7×10-7 19115949 (PMID) GRASP2 nonQTL
HIV-1 infection (natural long-term nonprogression) 1.2×10-6 22238471 (PMID) GRASP2 nonQTL
Height (adult females) 1.5×10-6 21194676 (PMID) GRASP2 nonQTL
HDL cholesterol 1.7×10-6 24097068 (PMID) Supplemental file
Differential exon level expression of HLA-B [probe 2948952] in peripheral blood mononuclear cells 2.4×10-6 19222302 (PMID) GRASP2 eQTL
Hip circumfence, adjusted for BMI 3.6×10-6 25673412 (PMID) Supplemental file
cholesterol 4.6×10-6 24816252 (PMID) gwas.eu via SNiPA
HIV-1-specific cross-reactive neutralizing activity 1.3×10-5 23372753 (PMID) GRASP2 nonQTL
Differential exon level expression of MICB [probe 2902359] in brain cortex 1.3×10-5 19222302 (PMID) GRASP2 eQTL
LDL cholesterol 2.1×10-5 24097068 (PMID) Supplemental file
Hip circumfence 3.7×10-5 25673412 (PMID) Supplemental file
Gene expression of MICA in CD4+ lymphocytes 5.8×10-5 20833654 (PMID) GRASP2 eQTL
Schizophrenia 1×10-4 19197363 (PMID) GRASP2 nonQTL
Type 2 diabetes 1.5×10-4 22885922 (PMID) Supplemental file
Crohn's disease 2×10-4 Supplemental file