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WCMC

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

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Locus annotations

Locus 233

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 rs16935432 11:18,470,487 G/A 0.14 996 0.516 0.060 1.9×10-17 1.900 9.8×10-18 4.2×10-10
SAA cis Replication rs78098319 11:18,404,299 G/A 0.18 337 0.389 0.099 1.1×10-4 1.590 1.2×10-4 0.002

 

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 (rs16935432) and 94 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
  • YWHABP2 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta pseudogene 2
  • LDHAL6A lactate dehydrogenase A-like 6A

 

Results from other genome-wide association studies

Trait P Study Source
cg23797887 (chr11:18477777) 8.8×10-146 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg07915343 (chr11:18477656) 2.4×10-32 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg00567382 (chr11:18473751) 2×10-17 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Baseline acute-phase serum amyloid concentrations 2.3×10-16 21124955 (PMID) GRASP2 nonQTL
Gene expression of LDHC in peripheral blood monocytes 2.1×10-7 20502693 (PMID) GRASP2 eQTL
cg14332815 (chr11:18433540) 2.8×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Amyotrophic lateral sclerosis (sporadic) 9×10-6 24529757 (PMID) GWAS Catalog via SNiPA
Gene expression of THEM4 in peripheral blood monocytes 9.3×10-6 20502693 (PMID) GRASP2 eQTL
cg02081001 (chr11:18720907) 1.6×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs

This locus links serum amyloid protein to amyotrophic lateral sclerosis (ALS).

This locus harbours a replicated cis-pQTL to Serum amyloid A-1 protein (SAA1). It is also a minor risk locus for Amyotrophic lateral sclerosis (sporadic) [PubMed]. Pre-Serum amyloid protein displayed different serum concentrations in ALS [PubMed].

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.