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

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Locus annotations

Locus 121

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 rs4150579 11:18,357,180 G/A 0.35 997 0.533 0.043 5.5×10-33 1.980 3×10-35 5.3×10-22
SAA cis Replication rs10741741 11:18,342,081 G/A 0.41 337 0.501 0.069 3.6×10-12 1.830 3.6×10-12 1.4×10-5

 

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 (rs4150579) and 47 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
  • HPS5 Hermansky-Pudlak syndrome 5
  • GTF2H1 general transcription factor IIH, polypeptide 1, 62kDa
Potentially regulated genes
eQTL genes
  • LDHA lactate dehydrogenase A
  • GTF2H1 general transcription factor IIH, polypeptide 1, 62kDa
  • SAA1 serum amyloid A1
  • HPS5 Hermansky-Pudlak syndrome 5
  • LDHC lactate dehydrogenase C

 

Results from other genome-wide association studies

Trait P Study Source
cg15585147 (chr11:18324522) 8.6×10-106 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Baseline acute-phase serum amyloid concentrations 1.7×10-51 21124955 (PMID) GRASP2 nonQTL
Amyloid A serum levels 2×10-51 21124955 (PMID) GWAS Catalog via SNiPA
alpha-hydroxyisovalerate 1.1×10-23 24816252 (PMID) gwas.eu via SNiPA
Gene expression of hCT1823757.2 in liver 1×10-15 18462017 (PMID) GRASP2 eQTL
"Gene expression of GTF2H1 [transcript NM_001142307, probe A_23_P36183] in liver" 6.7×10-15 21637794 (PMID) GRASP2 eQTL
Gene expression of HPS5 in peripheral blood monocytes 8.2×10-15 20502693 (PMID) GRASP2 eQTL
Gene expression of GTF2H1 in peripheral blood monocytes 2×10-13 20502693 (PMID) GRASP2 eQTL
PC aa C30:0 / PC aa C34:1 4.4×10-7 20037589 (PMID) GRASP2 metabQTL
Gene expression of HPS5 (ENSG00000110756) in dendritic cells 4×10-6 22233810 (PMID) GRASP2 eQTL
Gene expression of GTF2H1 in blood 5.9×10-6 21829388 (PMID) GRASP2 eQTL
Survival in pancreatic cancer 7.8×10-6 23180869 (PMID) GRASP2 nonQTL
PANCREATIC CANCER 9×10-6 23180869 (PMID) GWAS Catalog via SNiPA
Gene expression of GTF2H1 in liver 1.2×10-5 18462017 (PMID) GRASP2 eQTL
Gene expression of HPS5 (ENSG00000110756) in dendritic cells treated with Mycobacterium tuberculosis 2.4×10-5 22233810 (PMID) GRASP2 eQTL
PC ae C30:0 3.9×10-4 20037589 (PMID) GRASP2 metabQTL