Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

M. C. Cornelis*, E. M. Byrne, T. Esko, M. A. Nalls, A. Ganna, N. Paynter, K. L. Monda, N. Amin, K. Fischer, F. Renstrom, J. S. Ngwa, V. Huikari, A. Cavadino, I. M. Nolte, A. Teumer, K. Yu, P. Marques-Vidal, R. Rawal, A. Manichaikul, M. K. WojczynskiJ. M. Vink, J. H. Zhao, G. Burlutsky, J. Lahti, V. Mikkila, R. N. Lemaitre, J. Eriksson, S. K. Musani, T. Tanaka, F. Geller, J. Luan, J. Hui, R. Maegi, M. Dimitriou, M. E. Garcia, W-K Ho, M. J. Wright, L. M. Rose, P. K. E. Magnusson, N. L. Pedersen, D. Couper, B. A. Oostra, A. Hofman, M. A. Ikram, H. Snieder, R. P. Stolk, L. Franke, J. Karjalainen, H-J Westra, B. H. R. Wolffenbuttel, Coffee & Caffeine Genetics Consort, Int Parkinson's Dis Genomics Conso, North Amer Brain Expression Consor, UK Brain Expression Consortium

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

126 Citations (Scopus)


Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91 462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in similar to 30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log(10)Bayes factor (BF) > 5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (P <5x10(-8)). Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee.

Original languageEnglish
Pages (from-to)647-656
Number of pages10
JournalMolecular Psychiatry
Issue number5
Publication statusPublished - May-2015


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