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

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Locus annotations

Locus 244

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
CPNE1 cis Discovery rs1204656 20:33,982,846 A/G 0.30 996 -0.393 0.047 1×10-16 -1.250 9.3×10-17 5.2×10-14
CPNE1 cis Replication rs4911178 20:33,952,620 G/A 0.49 337 0.206 0.046 9.6×10-6 1.240 6.4×10-6 4.9×10-4

 

Regional association plots

 

Boxplots and histograms for top associations

Copine-1 (CPNE1)

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

Copine-1 (CPNE1)

Target (abbrv.) CPNE1
Target (full name) Copine-1
Somalogic ID (Sequence ID) SL011808 (5346-24_3)
Entrez Gene Symbol CPNE1
UniProt ID Q99829
UniProt Comment
  • Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes (PubMed:14674885). Involved in the TNF-alpha receptor signaling pathway in a calcium-dependent manner (PubMed:14674885). Exhibits calcium-dependent phospholipid binding properties (PubMed:9430674, PubMed:19539605). Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner (PubMed:23263657, PubMed:25450385). May recruit target proteins to the cell membrane in a calcium-dependent manner (PubMed:12522145). May function in membrane trafficking (PubMed:9430674). Involved in TNF-alpha-induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit (PubMed:18212740). Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL (PubMed:18212740).
Reactome
  • Glycerophospholipid biosynthesis

All locus annotations are based on the sentinel SNP (rs1204656) and 38 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
  • UQCC1 ubiquinol-cytochrome c reductase complex assembly factor 1
  • GDF5OS growth differentiation factor 5 opposite strand
  • GDF5 growth differentiation factor 5
Potentially regulated genes
  • ERGIC3 ERGIC and golgi 3
  • FER1L4 fer-1-like family member 4, pseudogene (functional)
  • MYH7B myosin, heavy chain 7B, cardiac muscle, beta
  • NFS1 NFS1 cysteine desulfurase
  • ACSS2 acyl-CoA synthetase short-chain family member 2
  • CPNE1 copine I
  • ROMO1 reactive oxygen species modulator 1
  • TRPC4AP transient receptor potential cation channel, subfamily C, member 4 associated protein
  • GSS glutathione synthetase
  • CEP250 centrosomal protein 250kDa
  • RBM12 RNA binding motif protein 12
eQTL genes
  • UQCC1 ubiquinol-cytochrome c reductase complex assembly factor 1
  • RPL36P4 ribosomal protein L36 pseudogene 4
  • FAM83C family with sequence similarity 83, member C
  • CEP250 centrosomal protein 250kDa
  • GDF5 growth differentiation factor 5
  • CPNE1 copine I
  • EIF6 eukaryotic translation initiation factor 6
  • GGT7 gamma-glutamyltransferase 7
  • MMP24-AS1 MMP24 antisense RNA 1
  • PROCR protein C receptor, endothelial
  • EDEM2 ER degradation enhancer, mannosidase alpha-like 2
  • ERGIC3 ERGIC and golgi 3

 

Results from other genome-wide association studies

Trait P Study Source
Height 4.8×10-91 25282103 (PMID) Supplemental file
Gene expression of UQCC in peripheral blood monocytes 3.8×10-29 20502693 (PMID) GRASP2 eQTL
Gene expression 3.9×10-25 20881960 (PMID) GRASP2 nonQTL
Hip circumfence, adjusted for BMI 6.3×10-15 25673412 (PMID) Supplemental file
Gene expression of CPNE1 in peripheral blood monocytes 4.5×10-9 20502693 (PMID) GRASP2 eQTL
Gene expression of UQCC in blood 3.4×10-8 21829388 (PMID) GRASP2 eQTL
Waist-to-hip ratio, adjusted for BMI 3.8×10-8 25673412 (PMID) Supplemental file
Hip circumfence 4×10-7 25673412 (PMID) Supplemental file
Waist-to-hip ratio 4.9×10-6 25673412 (PMID) Supplemental file
Gene expression of UQCC (ENSG00000101019) in dendritic cells treated with Mycobacterium tuberculosis 5.4×10-6 22233810 (PMID) GRASP2 eQTL
Gene expression of USP27X in peripheral blood monocytes 6.3×10-6 20502693 (PMID) GRASP2 eQTL
Pubertal growth, height at age 10 (girls) and 12 (boys) 7×10-5 23449627 (PMID) Supplemental file
Waist hip ratio 8×10-5 20935629 (PMID) GRASP2 nonQTL
cg14353508 (chr20:34207730) 1×10-4 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Total cholesterol 1.3×10-4 20686565 (PMID) GRASP2 nonQTL
Gene expression of CEP250 in blood 1.7×10-4 21829388 (PMID) GRASP2 eQTL
Gene expression of EDEM2 in blood 2.7×10-4 21829388 (PMID) GRASP2 eQTL
Triglycerides 2.9×10-4 24097068 (PMID) Supplemental file