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

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Locus annotations

Locus 146

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
MICB cis Discovery rs2905736 6:31,453,290 G/A 0.03 997 1.367 0.122 1.8×10-27 1.610 2.9×10-14 0.893

 

Regional association plots

MHC class I polypeptide-related sequence B (MICB)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

MHC class I polypeptide-related sequence B (MICB)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study

MHC class I polypeptide-related sequence B (MICB)

Target (abbrv.) MICB
Target (full name) MHC class I polypeptide-related sequence B
Somalogic ID (Sequence ID) SL005200 (5102-55_3)
Entrez Gene Symbol MICB
UniProt ID Q29980
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 (rs2905736) and 46 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
  • HCP5 HLA complex P5 (non-protein coding)
  • XXbac-BPG181B23.6
  • MICB MHC class I polypeptide-related sequence B
  • Y_RNA
  • XXbac-BPG16N22.5
  • PPIAP9 peptidylprolyl isomerase A (cyclophilin A) pseudogene 9
  • RPL15P4 ribosomal protein L15 pseudogene 4
  • MCCD1 mitochondrial coiled-coil domain 1
  • SNORD117 small nucleolar RNA, C/D box 117
  • ATP6V1G2-DDX39B ATP6V1G2-DDX39B readthrough (NMD candidate)
  • DDX39B DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
  • AL662801.1
  • ATP6V1G2 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2
  • DDX39B-AS1 DDX39B antisense RNA 1
  • SNORD84 small nucleolar RNA, C/D box 84
  • NFKBIL1 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1
  • TNF tumor necrosis factor
  • LTB lymphotoxin beta (TNF superfamily, member 3)
  • LTA lymphotoxin alpha
  • LST1 leukocyte specific transcript 1
  • NCR3 natural cytotoxicity triggering receptor 3
  • SNORA38 small nucleolar RNA, H/ACA box 38
  • PRRC2A proline-rich coiled-coil 2A
  • BAG6 BCL2-associated athanogene 6
  • Y_RNA
  • CSNK2B casein kinase 2, beta polypeptide
  • GPANK1 G patch domain and ankyrin repeats 1
  • LY6G5B lymphocyte antigen 6 complex, locus G5B
  • CSNK2B-LY6G5B--991
  • C6orf47-AS1 C6orf47 antisense RNA 1
  • C6orf47 chromosome 6 open reading frame 47
  • CLIC1 chloride intracellular channel 1
  • MSH5 mutS homolog 5
  • MSH5-SAPCD1 MSH5-SAPCD1 readthrough (NMD candidate)
  • VARS valyl-tRNA synthetase
  • Y_RNA
Potentially regulated genes
eQTL genes
  • XXbac-BPG181B23.7
  • TNXA tenascin XA (pseudogene)
  • NOTCH4 notch 4
  • MICB MHC class I polypeptide-related sequence B
  • MICA MHC class I polypeptide-related sequence A
  • LST1 leukocyte specific transcript 1
  • PSORS1C2 psoriasis susceptibility 1 candidate 2
  • DDR1 discoidin domain receptor tyrosine kinase 1
  • CDSN corneodesmosin
  • HLA-DRB6 major histocompatibility complex, class II, DR beta 6 (pseudogene)
  • RNF5 ring finger protein 5, E3 ubiquitin protein ligase

 

Results from other genome-wide association studies

Trait P Study Source
HIV-1 control (viral load at set point) 4.5×10-35 20041166 (PMID) GRASP2 nonQTL
HIV-1 control 4.5×10-35 20205591 (PMID) GRASP2 nonQTL
Drug-induced liver injury due to Flucloxacillin 8.7×10-33 20676096 (PMID) GRASP2 nonQTL
Flucloxacillin drug-induced liver injury 8.7×10-33 19483685 (PMID) GRASP2 nonQTL
Drug-induced liver injury (flucloxacillin) 9×10-33 19483685 (PMID) GWAS Catalog via SNiPA
Psoriasis 2×10-26 18369459 (PMID) GWAS Catalog via SNiPA
HIV-1 control (elite control) 4.1×10-23 21051598 (PMID) GRASP2 nonQTL
AIDS progression 3×10-19 19115949 (PMID) GWAS Catalog via SNiPA
HIV-1 seropositive nonprogression 3×10-19 19115949 (PMID) GRASP2 nonQTL
HIV-1 control (viral load) 3.2×10-19 21490045 (PMID) GRASP2 nonQTL
Rheumatoid arthritis 1.9×10-13 20453842 (PMID) GRASP2 nonQTL
HIV-1 disease progression 1.2×10-11 20041166 (PMID) GRASP2 nonQTL
HIV-1 infection (natural long-term nonprogression) 1.6×10-11 22238471 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all female DILI cases and controls 6.2×10-11 22968431 (PMID) GRASP2 nonQTL
Psoriatic arthritis 8×10-11 20953186 (PMID) GRASP2 nonQTL
Crohn's disease 4.6×10-10 Supplemental file
Drug-induced liver injury-all DILI cases presenting with any of three recorded extrahepatic immuno-allergic features (eosinophilia, fever, and/or rash) 4.9×10-10 22968431 (PMID) GRASP2 nonQTL
HIV-1 seropositive nonprogression (males) 8.7×10-10 19115949 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all DILI cases with time to onset less than or equal to the median of 24 days 2.5×10-8 22968431 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all DILI cases presenting with fever 3.3×10-8 22968431 (PMID) GRASP2 nonQTL
Drug-induced liver injury-to all DILI cases with age of onset greater than the median of 57.5 years 4.3×10-8 22968431 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all cholestatic DILI cases 1.2×10-7 22968431 (PMID) GRASP2 nonQTL
Psoriasis and/or psoriatic arthritis 1.4×10-7 18369459 (PMID) GRASP2 nonQTL
Psoriasis only (no arthritis) 6.2×10-7 18369459 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all DILI cases presenting with rash 2.9×10-6 22968431 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (geographic atrophy) 1×10-5 23455636 (PMID) GRASP2 nonQTL
Gene expression of MICA (probeID ILMN_1797929) in cerebellum in Alzheimer's disease cases and controls 1.7×10-5 22685416 (PMID) GRASP2 eQTL
Triglycerides 2.5×10-5 24097068 (PMID) Supplemental file
Total cholesterol 3×10-5 20686565 (PMID) GRASP2 nonQTL
Gene expression of MICA (probeID ILMN_1797929) in cerebellum in Alzheimer's disease cases 4.5×10-5 22685416 (PMID) GRASP2 eQTL
Drug-induced liver injury-all mixed injury DILI cases 5×10-5 22968431 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all DILI cases with age of onset less than or equal to the median of 57.5 years 7.2×10-5 22968431 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration 1.1×10-4 23455636 (PMID) GRASP2 nonQTL
LDL cholesterol 2.3×10-4 20686565 (PMID) GRASP2 nonQTL
Drug-induced liver injury-all DILI cases with time to onset greater than the median of 24 days 3×10-4 22968431 (PMID) GRASP2 nonQTL
Irritible bowel syndrome 3.2×10-4 18587394 (PMID) GRASP2 nonQTL
Ulcerative collitis 4.5×10-4 Supplemental file
Drug-induced liver injury-all hepatocellular DILI case 5×10-4 22968431 (PMID) GRASP2 nonQTL