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

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Locus annotations

Locus 126

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
GPVI cis Discovery rs1654439 19:55,553,647 G/T 0.17 996 -0.657 0.055 6.6×10-31 -1.200 6.3×10-31 1.2×10-26
GPVI cis Replication rs1671152 19:55,526,345 C/A 0.20 337 -0.191 0.045 2.4×10-5 -1.150 2×10-6 5.1×10-11

 

Regional association plots

 

Boxplots and histograms for top associations

Platelet glycoprotein VI (GPVI)

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

Platelet glycoprotein VI (GPVI)

Target (abbrv.) GPVI
Target (full name) Platelet glycoprotein VI
Somalogic ID (Sequence ID) SL008759 (3194-36_2)
Entrez Gene Symbol GP6
UniProt ID Q9HCN6
UniProt Comment
  • Collagen receptor involved in collagen-induced platelet adhesion and activation. Plays a key role in platelet procoagulant activity and subsequent thrombin and fibrin formation. This procoagulant function may contribute to arterial and venous thrombus formation. The signaling pathway involves the FcR gamma-chain, the Src kinases (likely Fyn/Lyn), the adapter protein LAT and leads to the activation of phospholipase C gamma2.
Reactome
  • Cell surface interactions at the vascular wall
  • GPVI-mediated activation cascade
  • Platelet Adhesion to exposed collagen

All locus annotations are based on the sentinel SNP (rs1654439) and 15 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
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg03354414 (chr19:55546142) 7.7×10-38 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of NLRP2 in peripheral blood monocytes 1.9×10-18 20502693 (PMID) GRASP2 eQTL
Gene expression of NLRP2 in blood 2.6×10-14 21829388 (PMID) GRASP2 eQTL
Gene expression of NLRP2 (probeID ILMN_1664878) in temporal cortex in Alzheimer's disease cases and controls 4.4×10-9 22685416 (PMID) GRASP2 eQTL
Gene expression of RDH13 in blood 8.4×10-8 21829388 (PMID) GRASP2 eQTL
Gene expression of EPS8L1 (probeID ILMN_1671600) in cerebellum in Alzheimer's disease cases and controls 5.2×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of NLRP2 (probeID ILMN_1664878) in temporal cortex in Alzheimer's disease cases 6.2×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of GP6 (probeID ILMN_2223772) in temporal cortex in Alzheimer's disease cases and controls 9.6×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of NLRP2 (probeID ILMN_1664878) in cerebellum in Alzheimer's disease cases and controls 9.3×10-6 22685416 (PMID) GRASP2 eQTL
Gene expression of EPS8L1 (probeID ILMN_1671600) in cerebellum in non-Alzheimer's disease samples 4.4×10-5 22685416 (PMID) GRASP2 eQTL