HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 58

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Coagulation Factor VII cis Discovery rs776905 13:113,781,942 A/C 0.11 997 -1.104 0.060 9.2×10-65 -1.340 2.2×10-69 2.2×10-42
Coagulation Factor VII cis Replication rs3093253 13:113,774,092 G/A 0.20 337 -1.234 0.063 5×10-57 -1.410 9.8×10-66 3×10-47

 

Regional association plots

 

Boxplots and histograms for top associations

Coagulation Factor VII

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

Coagulation Factor VII

Target (abbrv.) Coagulation Factor VII
Target (full name) Coagulation Factor VII
Somalogic ID (Sequence ID) SL000358 (3184-25_2)
Entrez Gene Symbol F7
UniProt ID P08709
UniProt Comment
  • Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.
Targeted by drugs (based on IPA annotation)
  • nematode anticoagulant protein c2
Biomarker applications (based on IPA annotation)
  • unspecified application
Wiki Pathways
  • Blood Clotting Cascade
  • Complement and Coagulation Cascades
  • Folate Metabolism
  • Selenium Pathway
  • Vitamin B12 Metabolism
Reactome
  • BMAL1:CLOCK,NPAS2 activates circadian gene expression
  • Extrinsic Pathway of Fibrin Clot Formation
  • Gamma-carboxylation of protein precursors
  • Removal of aminoterminal propeptides from gamma-carboxylated proteins
  • Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus
Pathway Studio
  • Coagulation Cascade
  • Vitamin K metabolism

All locus annotations are based on the sentinel SNP (rs776905) and 2 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
  • F10 coagulation factor X
  • F10-AS1 F10 antisense RNA 1
  • KARSP2 lysyl-tRNA synthetase pseudogene 2
eQTL genes
  • F10 coagulation factor X
  • F7 coagulation factor VII (serum prothrombin conversion accelerator)

 

Results from other genome-wide association studies

Trait P Study Source
Prothrombin time by INR (international normalized ratio) 4×10-46 22703881 (PMID) GRASP2 nonQTL
Factor VII clotting activity 9.7×10-35 23381943 (PMID) GRASP2 nonQTL
Factor X antigen 5×10-14 23381943 (PMID) GRASP2 nonQTL
cg15672437 (chr13:113764531) 4.1×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg26593267 (chr13:113764847) 3.3×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
P08709 protein abundance levels 4.3×10-5 22595970 (PMID) GRASP2 pQTL
cg06925625 (chr13:113887585) 1.3×10-4 10.1101/033084 (DOI) BIOS QTL cis-meQTLs