A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Research output: Contribution to journalJournal articlepeer-review

  • Shweta Ramdas
  • Jonathan Judd
  • Sarah E. Graham
  • Stavroula Kanoni
  • Yuxuan Wang
  • Ida Surakka
  • Brandon Wenz
  • Shoa L. Clarke
  • Alessandra Chesi
  • Andrew Wells
  • Konain Fatima Bhatti
  • Sailaja Vedantam
  • Thomas W. Winkler
  • Adam E. Locke
  • Eirini Marouli
  • Greg J.M. Zajac
  • Kuan Han H. Wu
  • Ioanna Ntalla
  • Qin Hui
  • Derek Klarin
  • Austin T. Hilliard
  • Zeyuan Wang
  • Chao Xue
  • Gudmar Thorleifsson
  • Anna Helgadottir
  • Daniel F. Gudbjartsson
  • Hilma Holm
  • Isleifur Olafsson
  • Mi Yeong Hwang
  • Sohee Han
  • Jing Hua Zhao
  • Aadahl, Mette
  • Jette Bork-Jensen
  • Line T. Møllehave
  • Jun Liu
  • Jun-Sing Wang
  • drb459, drb459
  • Rebecca D Jackson
  • Peter Kovacs
  • Pedersen, Oluf Borbye
  • Hansen, Torben
  • Lars Lind
  • Loos, Ruth
  • Kaare Christensen
  • Linneberg, Allan René
  • Grarup, Niels
  • Thomas M. Dantoft
  • Fredrik Karpe
  • Wei Qi Wei
  • Yan V. Sun
  • Million Veterans Program
  • Global Lipids Genetics Consortium

A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.

Original languageEnglish
JournalAmerican Journal of Human Genetics
Issue number8
Pages (from-to)1366-1387
Number of pages22
Publication statusPublished - 2022

Bibliographical note

Publisher Copyright:
© 2022 American Society of Human Genetics

    Research areas

  • complex traits, fine-mapping, functional genomics, lipid biology, post-GWAS, regulatory mechanism, variant prioritization

ID: 319153369