A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology

Paul S. de Vries, Maria Sabater-Lleal, Jennifer E. Huffman, Jonathan Marten, Ci Song, Nathan Pankratz, Traci M. Bartz, Hugoline G. de Haan, Graciela E. Delgado, John D. Eicher, Angel Martinez-Perez, Cavin K. Ward-Caviness, Jennifer A. Brody, Ming-Huei Chen, Moniek P. M. de Maat, Mattias Frånberg, Dipender Gill, Marcus E. Kleber, Fernando Rivadeneira, José Manuel Soria, Weihong Tang, Geoffrey H. Tofler, André G. Uitterlinden, Astrid van Hylckama Vlieg, Sudha Seshadri, Eric Boerwinkle, Neil M. Davies, Anne-Katrin Giese, M. Kamran Ikram, Steven J. Kittner, Barbara McKnight, Bruce M. Psaty, Alex P. Reiner, Muralidharan Sargurupremraj, Kent D. Taylor, INVENT Consortium, MEGASTROKE Consortium of the International Stroke Genetics Consortium, Myriam Fornage, Anders Hamsten, Winfried März, Frits R. Rosendaal, Juan Carlos Souto, Abbas Dehghan, Andrew D. Johnson, Alanna C. Morrison, Christopher J. O'Donnell and Nicholas L. Smith

Key Points

  • We identify 2 new genetic loci associated with FVII activity and highlight REEP3 and JAZF1 as potential underlying causal genes.

  • We provide evidence for a causal effect of FVII activity on the risk of IS.


Factor VII (FVII) is an important component of the coagulation cascade. Few genetic loci regulating FVII activity and/or levels have been discovered to date. We conducted a meta-analysis of 9 genome-wide association studies of plasma FVII levels (7 FVII activity and 2 FVII antigen) among 27 495 participants of European and African ancestry. Each study performed ancestry-specific association analyses. Inverse variance weighted meta-analysis was performed within each ancestry group and then combined for a trans-ancestry meta-analysis. Our primary analysis included the 7 studies that measured FVII activity, and a secondary analysis included all 9 studies. We provided functional genomic validation for newly identified significant loci by silencing candidate genes in a human liver cell line (HuH7) using small-interfering RNA and then measuring F7 messenger RNA and FVII protein expression. Lastly, we used meta-analysis results to perform Mendelian randomization analysis to estimate the causal effect of FVII activity on coronary artery disease, ischemic stroke (IS), and venous thromboembolism. We identified 2 novel (REEP3 and JAZF1-AS1) and 6 known loci associated with FVII activity, explaining 19.0% of the phenotypic variance. Adding FVII antigen data to the meta-analysis did not result in the discovery of further loci. Silencing REEP3 in HuH7 cells upregulated FVII, whereas silencing JAZF1 downregulated FVII. Mendelian randomization analyses suggest that FVII activity has a positive causal effect on the risk of IS. Variants at REEP3 and JAZF1 contribute to FVII activity by regulating F7 expression levels. FVII activity appears to contribute to the etiology of IS in the general population.

  • Submitted May 8, 2018.
  • Accepted December 6, 2018.
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