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. 2017 Mar 29;49:35. doi: 10.1186/s12711-017-0311-8

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© The Author(s) 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 3 — Manhattan plots from three methods of genome-wide association analysis. a Manhattan plot of p values for testing additive SNP effects using the generalized least squares (GLS) analysis of EPISNP2. b Manhattan plot of p values for testing dominance SNP effects using the generalized least squares (GLS) analysis of EPISNP2. c Manhattan plot of p values for testing additive SNP effects using the least squares (LS) analysis of PLINK with the first 35 dimensions of multidimensional scaling (MDS) as fixed effects. d Manhattan plot of p values for testing additive SNP effects using the LS analysis of EPISNP1 with the first 35 MDS dimensions as fixed effects. The horizontal green line indicates the genome-wide significance with the Bonferroni correction (p < 10^−5.91). All p values in the figures are in log(1/p) scale