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

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Locus annotations

Locus 342

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 rs2523987 6:30,079,993 A/C 0.11 996 0.496 0.067 2.4×10-13 1.370 2.4×10-11 6.6×10-6
MICA cis Replication rs2844793 6:30,080,496 G/A 0.07 337 -0.009 0.141 0.95 1.000 0.994 0.784

 

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 (rs2523987) and 27 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
  • ZNRD1-AS1 ZNRD1 antisense RNA 1
  • HLA-J major histocompatibility complex, class I, J (pseudogene)
  • HLA-F major histocompatibility complex, class I, F
  • TRIM31 tripartite motif containing 31
  • HLA-F-AS1 HLA-F antisense RNA 1
  • LINC00243
  • HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1
  • TRIM31-AS1 TRIM31 antisense RNA 1
  • HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
  • HLA-H major histocompatibility complex, class I, H (pseudogene)
  • HLA-C major histocompatibility complex, class I, C
  • HLA-V major histocompatibility complex, class I, V (pseudogene)
  • PPP1R11 protein phosphatase 1, regulatory (inhibitor) subunit 11
  • HLA-U major histocompatibility complex, class I, U (pseudogene)
  • BTN3A3 butyrophilin, subfamily 3, member A3
  • BTN3A2 butyrophilin, subfamily 3, member A2
  • HLA-G major histocompatibility complex, class I, G
  • ZFP57 ZFP57 zinc finger protein
  • IER3 immediate early response 3
  • HIST1H3I histone cluster 1, H3i
  • HCG4P11 HLA complex group 4 pseudogene 11
  • HLA-A major histocompatibility complex, class I, A
  • PPP1R18 protein phosphatase 1, regulatory subunit 18
  • HCG22 HLA complex group 22
  • HLA-K major histocompatibility complex, class I, K (pseudogene)

 

Results from other genome-wide association studies

Trait P Study Source
Myasthenia gravis 3.4×10-71 23055271 (PMID) GRASP2 nonQTL
Gene expression of BTN3A2 in peripheral blood monocytes 9.7×10-36 20502693 (PMID) GRASP2 eQTL
Idiopathic membranous nephropathy 1.1×10-21 21323541 (PMID) GRASP2 nonQTL
Gene expression of TRIM10 in blood 5.4×10-20 21829388 (PMID) GRASP2 eQTL
Gene expression of HLA-DRB4 in peripheral blood monocytes 3.5×10-16 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-A29.1 in peripheral blood monocytes 7.1×10-13 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DQA1 in peripheral blood monocytes 7.6×10-13 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-G in peripheral blood monocytes 5.1×10-12 20502693 (PMID) GRASP2 eQTL
Type 1 diabetes 8.1×10-11 17632545 (PMID) GRASP2 nonQTL
Gene expression of ZFP57 in peripheral blood monocytes 1×10-10 20502693 (PMID) GRASP2 eQTL
Schizophrenia 4.9×10-10 23974872 (PMID) Supplemental file
Gene expression of HLA-DRB1 in peripheral blood monocytes 6.3×10-10 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-A in peripheral blood monocytes 1.1×10-9 20502693 (PMID) GRASP2 eQTL
Lung cancer 1.7×10-9 22899653 (PMID) GRASP2 nonQTL
Gene expression of HLA-DQB1 [probe 209480_at] in lymphoblastoid cell lines 1.8×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of XRCC6 in blood 2.7×10-9 21829388 (PMID) GRASP2 eQTL
Type 1 diabetes, Rheumatoid arthritis, combined case analysis 4×10-9 17554300 (PMID) GRASP2 nonQTL
Rheumatoid arthritis 4×10-9 20453842 (PMID) GRASP2 nonQTL
Gene expression of HCG27 in peripheral blood monocytes 7.3×10-9 20502693 (PMID) GRASP2 eQTL
Gene expression of BTN3A2 [probe 209846_s_at] in lymphoblastoid cell lines 7.6×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of HLA-H in blood 1.5×10-8 21829388 (PMID) GRASP2 eQTL
Gene expression of VARS2 in peripheral blood monocytes 3.4×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DQA1 [probe 203290_at] in lymphoblastoid cell lines 3.5×10-8 17873877 (PMID) GRASP2 eQTL
Gene expression of HLA-DQA1 [probe 213831_at] in lymphoblastoid cell lines 7.1×10-8 17873877 (PMID) GRASP2 eQTL
Bipolar disorder vs. Schizophrenia 7.3×10-8 24280982 (PMID) Supplemental file
Gene expression of HLA-C [probe 216526_x_at] in lymphoblastoid cell lines 9.6×10-8 17873877 (PMID) GRASP2 eQTL
Gene expression of HLA-DQB1 in peripheral blood monocytes 1×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DPB1 in peripheral blood monocytes 4.4×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of ZKSCAN4 in peripheral blood monocytes 4.5×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of APOM in peripheral blood monocytes 1.9×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of HLA-DRB5 in peripheral blood monocytes 4.6×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of TRIM31 in normal prepouch ileum 1.9×10-5 23474282 (PMID) GRASP2 eQTL
Cardiac neonatal lupus 2×10-5 20662065 (PMID) GRASP2 nonQTL
Cross-disorder, subset Schizophrenia 3×10-5 23453885 (PMID) Supplemental file
Head Circumfence 3.8×10-5 22504419 (PMID) Supplemental file
Infant head circumference 3.8×10-5 22504419 (PMID) GRASP2 nonQTL
Transmission distortion 5.7×10-5 22377632 (PMID) GRASP2 nonQTL
Total cholesterol 8.3×10-5 24097068 (PMID) Supplemental file
Gene expression of [probe 2450326 centered at chr6:30023353] in blood 1×10-4 21829388 (PMID) GRASP2 eQTL
Crohn's disease 1.8×10-4 Supplemental file
Gene expression of TRIM26 in blood 3.8×10-4 21829388 (PMID) GRASP2 eQTL