HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 245

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 rs3134942 6:32,168,771 G/T 0.11 994 0.579 0.069 1.2×10-16 1.440 7×10-14 7.1×10-6
MICA cis Replication rs3134942 6:32,168,771 C/A 0.05 337 -0.034 0.163 0.836 -1.030 0.702 0.491

 

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 (rs3134942) and 5 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.

Linked genes

Genes hit or close-by
Potentially regulated genes
eQTL genes
  • HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
  • HLA-DQB2 major histocompatibility complex, class II, DQ beta 2
  • C4A complement component 4A (Rodgers blood group)
  • HLA-C major histocompatibility complex, class I, C
  • HLA-E major histocompatibility complex, class I, E
  • CYP21A2 cytochrome P450, family 21, subfamily A, polypeptide 2
  • BTN3A2 butyrophilin, subfamily 3, member A2
  • MICB MHC class I polypeptide-related sequence B
  • VARS2 valyl-tRNA synthetase 2, mitochondrial
  • HCG27 HLA complex group 27 (non-protein coding)
  • HLA-DRB5 major histocompatibility complex, class II, DR beta 5
  • NOTCH4 notch 4
  • RNF5 ring finger protein 5, E3 ubiquitin protein ligase
  • HLA-DMA major histocompatibility complex, class II, DM alpha
  • C4B complement component 4B (Chido blood group)
  • WASF5P WAS protein family, member 5, pseudogene
  • HLA-DPB1 major histocompatibility complex, class II, DP beta 1
  • CYP21A1P cytochrome P450, family 21, subfamily A, polypeptide 1 pseudogene

 

Results from other genome-wide association studies

Trait P Study Source
cg01620082 (chr3:125678431) 1.7×10-105 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17862947 (chr12:133086950) 9.6×10-100 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06606381 (chr12:133084921) 8.5×10-94 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Type 1 diabetes, combined control dataset 2×10-82 17554300 (PMID) GRASP2 nonQTL
Complement C3 and C4 levels 4×10-72 23028341 (PMID) GWAS Catalog via SNiPA
Serum Complement C4 4.3×10-72 23028341 (PMID) GRASP2 nonQTL
Gene expression of HLA-DRB5 (probeID ILMN_1701686) in whole blood 1.4×10-45 22692066 (PMID) GRASP2 eQTL
Gene expression of HLA-DRB4 in peripheral blood monocytes 5.3×10-45 20502693 (PMID) GRASP2 eQTL
cg01255021 (chr16:1094629) 1.1×10-33 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg02753903 (chr19:38943549) 7.5×10-31 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17841099 (chr1:153940066) 3.1×10-27 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-DRB1 in peripheral blood monocytes 6.6×10-27 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DQB1 in peripheral blood monocytes 6×10-24 20502693 (PMID) GRASP2 eQTL
cg22379212 (chr19:38944024) 2.1×10-18 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg00624589 (chr16:1094766) 2.1×10-18 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Schizophrenia 1.9×10-16 25056061 (PMID) Supplemental file
cg06099246 (chr16:1094837) 3.4×10-16 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg23331010 (chr3:98512714) 1.8×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19808620 (chr1:153514466) 4.8×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg18651192 (chr3:125677598) 5.9×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg07575812 (chr5:138883534) 7.8×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of BTN3A2 in peripheral blood monocytes 2.2×10-14 20502693 (PMID) GRASP2 eQTL
Gene expression of HCG27 in peripheral blood monocytes 2.7×10-14 20502693 (PMID) GRASP2 eQTL
cg15007120 (chr3:109128526) 7.6×10-14 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-DRB5 in peripheral blood monocytes 1.7×10-12 20502693 (PMID) GRASP2 eQTL
cg22322277 (chr6:75459134) 2.1×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-C in peripheral blood monocytes 5.9×10-12 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DPB1 in peripheral blood monocytes 7.4×10-12 20502693 (PMID) GRASP2 eQTL
cg23656755 (chr1:230203067) 8.3×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19589727 (chr20:57427786) 1.1×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-DQA1 in peripheral blood monocytes 1.3×10-11 20502693 (PMID) GRASP2 eQTL
cg03908391 (chr20:57427194) 2.3×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg20495738 (chr12:2338423) 4.2×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Triglycerides 1.3×10-10 24097068 (PMID) Supplemental file
cg19313311 (chr7:74058055) 1.5×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Rheumatoid arthritis 1.5×10-10 20453842 (PMID) GRASP2 nonQTL
cg19640589 (chr20:57427997) 1.8×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg26534489 (chr20:57427519) 4.6×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg04010868 (chr16:11876357) 5.1×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg01970336 (chr1:51986230) 6.7×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg14066773 (chr19:2234238) 9.6×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Rheumatoid arthritis (ACPA-positive) 1.3×10-9 21156761 (PMID) GRASP2 nonQTL
cg08065963 (chr16:8985569) 1.7×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg27661264 (chr20:57427762) 2.6×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg10302550 (chr20:57427845) 2.6×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg05277504 (chr17:79961638) 2.9×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg12321149 (chr20:57427402) 3.1×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg14564778 (chr20:57427532) 3.6×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Total cholesterol 3.9×10-9 24097068 (PMID) Supplemental file
cg17414107 (chr20:57427854) 4.7×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg01817393 (chr20:57427618) 5.1×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg07408552 (chr17:40612019) 5.1×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg01017090 (chr20:57427022) 6.8×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06406458 (chr10:128810523) 8.6×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg20954971 (chr21:44593666) 9.8×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg12494529 (chr10:1082456) 1.1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg27050612 (chr17:46133222) 1.2×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22157027 (chr2:10638089) 1.4×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06065549 (chr20:57427419) 1.5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg04788957 (chr10:105438032) 1.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg05946118 (chr16:8985614) 2.3×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg04257105 (chr20:57427689) 2.5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg14153654 (chr1:8001003) 2.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg20528838 (chr20:57427754) 2.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17467525 (chr1:9686499) 2.8×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22290117 (chr20:57427197) 3.6×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg23052776 (chr14:71609182) 3.6×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg09222732 (chr6:466917) 3.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg00943909 (chr20:57427966) 5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg03722901 (chr19:6429783) 5.3×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg21333217 (chr3:129277297) 5.9×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg03708907 (chr19:38943310) 9.8×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg12342742 (chr11:64835016) 9.8×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg24854010 (chr12:1726057) 1.1×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg18857369 (chr14:105518224) 1.2×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-DRB3 in peripheral blood monocytes 1.3×10-7 20502693 (PMID) GRASP2 eQTL
cg23290159 (chr5:150474258) 1.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg18810022 (chr2:134989787) 1.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg04571189 (chr2:10638048) 2×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg24137511 (chr19:18260306) 2.1×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg08071700 (chr16:81579268) 2.3×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg07441944 (chr11:44623435) 2.5×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg07992484 (chr2:106724137) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg25719851 (chr12:7055428) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of APOM in peripheral blood monocytes 2.7×10-7 20502693 (PMID) GRASP2 eQTL
Height 6.7×10-7 25282103 (PMID) Supplemental file
Gene expression of VARS2 in peripheral blood monocytes 2.5×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-G in peripheral blood monocytes 6.1×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of FASTKD2 in peripheral blood monocytes 7.1×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-A in peripheral blood monocytes 7.8×10-6 20502693 (PMID) GRASP2 eQTL
Bipolar disorder vs. Schizophrenia 4.9×10-5 24280982 (PMID) Supplemental file
Gene expression of SNORD52 in normal prepouch ileum 6.3×10-5 23474282 (PMID) GRASP2 eQTL
Cross-disorder, subset Schizophrenia 1.9×10-4 23453885 (PMID) Supplemental file
LDL cholesterol 2.2×10-4 24097068 (PMID) Supplemental file