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

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Locus annotations

Locus 262

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Calcineurin cis Discovery rs17266357 4:102,721,809 T/C 0.31 997 0.368 0.045 8.7×10-16 1.120 7.6×10-14 1.1×10-14
Calcineurin cis Replication rs4699262 4:102,726,005 G/A 0.19 337 0.131 0.048 0.007 1.090 0.002 0.001

 

Regional association plots

 

Boxplots and histograms for top associations

Calcineurin

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

Calcineurin

Target (abbrv.) Calcineurin
Target (full name) Calcineurin
Somalogic ID (Sequence ID) SL003657 (4903-72_1)
Entrez Gene Symbol PPP3CA, PPP3R1
UniProt ID Q08209, P63098
UniProt Comment
  • Q08209: Calcium-dependent, calmodulin-stimulated protein phosphatase. Many of the substrates contain a PxIxIT motif. This subunit may have a role in the calmodulin activation of calcineurin. Dephosphorylates DNM1L, HSPB1 and SSH1.
  • P63098: Regulatory subunit of calcineurin, a calcium-dependent, calmodulin stimulated protein phosphatase. Confers calcium sensitivity.
Targeted by drugs (based on IPA annotation)
  • cyclosporin A
Wiki Pathways
  • Alzheimers Disease
  • Energy Metabolism
  • G Protein Signaling Pathways
  • Lymphocyte TarBase
  • MAPK signaling pathway
  • MicroRNAs in cardiomyocyte hypertrophy
  • Mitochondrial Gene Expression
  • Muscle cell TarBase
  • Physiological and Pathological Hypertrophy of the Heart
Pathway Interaction Database
  • BCR signaling pathway
  • C-MYB transcription factor network
  • Calcium signaling in the CD4+ TCR pathway
  • Downstream signaling in naïve CD8+ T cells
  • IL12 signaling mediated by STAT4
  • IL12-mediated signaling events
  • Role of Calcineurin-dependent NFAT signaling in lymphocytes
Reactome
  • CLEC7A (Dectin-1) induces NFAT activation
  • Ca2+ pathway
  • DARPP-32 events
  • FCERI mediated Ca+2 mobilization

All locus annotations are based on the sentinel SNP (rs17266357) and 48 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


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Genes hit or close-by
  • BANK1 B-cell scaffold protein with ankyrin repeats 1
eQTL genes
  • BANK1 B-cell scaffold protein with ankyrin repeats 1

 

Results from other genome-wide association studies

Trait P Study Source
cg00332153 (chr4:102712034) 3.2×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of BANK1 in blood 5.7×10-5 21829388 (PMID) GRASP2 eQTL
Type 1 diabetes, Rheumatoid arthritis, Crohn's disease, combined case analysis, gender differentiated 1.6×10-4 17554300 (PMID) GRASP2 nonQTL
Body mass index 1.7×10-4 25673413 (PMID) Supplemental file
Systemic lupus erythematosus (SLE) 3.2×10-4 23273568 (PMID) GRASP2 nonQTL