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Phantom epistasis between unlinked loci

The Original Article was published on 26 February 2014

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Data availability

The gene expression data used to generate the original H2014 paper is available at the Gene Expression Omnibus (GEO) under accession code GSE53195. The ALSPAC genotype data can be accessed via This study makes use of data from dbGaP (accessions phs000428.v1.p1) and EGA (accessions EGAS00001000108 and EGAS00001000090) (see Supplementary Information for a full list of acknowledgements to these datasets).

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Code is available at:


  1. Hemani, G. et al. Detection and replication of epistasis influencing transcription in humans. Nature 508, 249–253 (2014).

    Article  ADS  CAS  Google Scholar 

  2. Wood, A. R. et al. Another explanation for apparent epistasis. Nature 514, E3–E5 (2014).

    Article  CAS  Google Scholar 

  3. Hemani, G. et al. Another explanation for apparent epistasis. Nature 514, E5 (2014).

    Article  CAS  Google Scholar 

  4. Hemani, G., Theocharidis, A., Wei, W. & Haley, C. EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics 27, 1462–1465 (2011).

    Article  CAS  Google Scholar 

  5. Cockerham, C. C. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39, 859–882 (1954).

    Article  CAS  Google Scholar 

  6. Cordell, H. J. Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 11, 2463–2468 (2002).

    Article  CAS  Google Scholar 

  7. Wei, W.-H., Hemani, G. & Haley, C. S. Detecting epistasis in human complex traits. Nat. Rev. Genet. 15, 722–733 (2014).

    Article  CAS  Google Scholar 

  8. Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).

    Article  Google Scholar 

  9. de los Campos, G., Sorensen, D. A. & Toro, M. A. imperfect linkage disequilibrium generates phantom epistasis (& perils of big data). G3 (Bethesda) 9, 1429–1436 (2019).

  10. Yang, J. et al. Genomic inflation factors under polygenic inheritance. Eur. J. Hum. Genet. 19, 807–812 (2011).

    Article  Google Scholar 

  11. Hemani, G. et al. Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs. Am. J. Hum. Genet. 93, 865–875 (2013).

    Article  CAS  Google Scholar 

  12. Gaunt, T. R. & Davey Smith, G. eNOS and coronary artery disease: publication bias and the eclipse of hypothesis-driven meta-analysis in genetic association studies. Gene 556, 257–258 (2015).

    Article  CAS  Google Scholar 

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G.H. was funded by the Wellcome Trust and Royal Society (208806/Z/17/Z). J.E.P. is supported by National Health and Medical Research Council Fellowship (APP1175781). J.Y. and P.M.V. are supported by the Australian Research Council (DP160101343, DP160101056, FT180100186 and FL180100072) and the Australian National Health and Medical Research Council (1078037, 1078901, 1113400 and 1107258). J.Y. is supported by the Westlake Education Foundation. We are extremely grateful to all the families who took part in the ALSPAC study, the midwives for their help in recruiting them, and the whole ALSPAC team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists and nurses.

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Authors and Affiliations



G.H., J.E.P., J.Y. and P.M.V. conceived the analyses. M.E.G. and P.M.V. developed the theory. G.H., J.E.P. and H.W. conducted the analyses. G.H., J.E.P., P.M.V., J.Y. and G.G. wrote the paper. All authors provided critical feedback on the interpretation of the results

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Correspondence to Gibran Hemani.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Notes 1-6, Supplementary Figures 1-9, and Supplementary References.

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Hemani, G., Powell, J.E., Wang, H. et al. Phantom epistasis between unlinked loci. Nature 596, E1–E3 (2021).

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