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WCMC

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

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Locus annotations

Locus 22

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
SAA cis Discovery rs1993373 11:18,280,635 G/A 0.34 997 0.917 0.037 2.2×10-105 3.390 7.1×10-128 1.3×10-48
SAA cis Replication rs4638289 11:18,285,774 A/T 0.49 337 -0.732 0.058 5.5×10-30 -2.470 4.3×10-32 7.8×10-9

 

Regional association plots

 

Boxplots and histograms for top associations

Serum amyloid A-1 protein (SAA)

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

Serum amyloid A-1 protein (SAA)

Target (abbrv.) SAA
Target (full name) Serum amyloid A-1 protein
Somalogic ID (Sequence ID) SL000572 (4336-2_1)
Entrez Gene Symbol SAA1
UniProt ID P0DJI8
UniProt Comment
  • Major acute phase protein.
Biomarker applications (based on IPA annotation)
  • diagnosis
  • unspecified application
Reactome
  • Advanced glycosylation endproduct receptor signaling
  • Amyloids
  • DEx/H-box helicases activate type I IFN and inflammatory cytokines production
  • Formyl peptide receptors bind formyl peptides and many other ligands
  • G alpha (i) signalling events
  • G alpha (q) signalling events
  • RIP-mediated NFkB activation via ZBP1
  • Scavenging by Class B Receptors
  • TAK1 activates NFkB by phosphorylation and activation of IKKs complex
  • TRAF6 mediated NF-kB activation

All locus annotations are based on the sentinel SNP (rs1993373) and 6 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
  • ST13P5 suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) pseudogene 5
  • SAA1 serum amyloid A1
  • RNA5SP334 RNA, 5S ribosomal pseudogene 334
Potentially regulated genes
  • TSG101 tumor susceptibility 101
  • PTPN5 protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)
  • HPS5 Hermansky-Pudlak syndrome 5
  • SAA1 serum amyloid A1
eQTL genes
  • SAA1 serum amyloid A1
  • SAA2 serum amyloid A2
  • SAA2-SAA4 SAA2-SAA4 readthrough
  • GTF2H1 general transcription factor IIH, polypeptide 1, 62kDa

 

Results from other genome-wide association studies

Trait P Study Source
Baseline acute-phase serum amyloid concentrations 2.8×10-53 21124955 (PMID) GRASP2 nonQTL
Amyloid A serum levels 3×10-53 21124955 (PMID) GWAS Catalog via SNiPA
Gene expression of RSE_00000802269 in liver 3.1×10-12 18462017 (PMID) GRASP2 eQTL
Lung cancer (squamous cell carcinoma) 8.8×10-6 23341777 (PMID) GRASP2 nonQTL
P02735 protein abundance levels 1×10-4 22595970 (PMID) GRASP2 pQTL
Gene expression of LDHC [probe ILMN_15784] in osteoblasts treated with dexamethasone 1.8×10-4 21283786 (PMID) GRASP2 eQTL
Gemcitabine toxicity as measured by gemcitabine IC50 in lymphoblastoid cell lines 2.2×10-4 19898621 (PMID) GRASP2 eQTL