Open Access Highly Accessed Research article

The genomic signature of trait-associated variants

Alida S D Kindt, Pau Navarro, Colin A M Semple and Chris S Haley*

Author Affiliations

MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, EH4 2XU, Edinburgh, UK

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BMC Genomics 2013, 14:108  doi:10.1186/1471-2164-14-108

Published: 18 February 2013

Additional files

Additional file 1:

Statistics of genomic features. Containing distribution statistics of the analyzed genomic features including number of sites, percentages of nucleotides covered, percentages of SNPs covered and the average length of the annotated nucleotide sites.

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Additional file 2:

Fold Enrichment for significantly trait-associated SNPs. Comparing odds ratios obtained by permutations, fold enrichment and obtained percentages for observed and permuted significantly trait-associated SNPs.

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Additional file 3:

Fold enrichment and odds ratios. Showing that Odds ratios and fold enrichment are strongly correlated with each other (r2 = 0.96). The correlation is highly significant (P-value = 7.8 × 10-40) indicating that odds ratios can be interpreted as fold enrichment.

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Additional file 4:

Different r2 threshold comparisons in genic regions. Showing the comparison between two different r2 thresholds for the genic regions. Overall the odds ratios do not show significant differences.

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Additional file 5:

Different r2 threshold comparisons in regions of conserved and evolutionary signatures. Showing the comparison between two different r2 thresholds for the conserved regions. Overall the odds ratios do not show significant differences.

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Additional file 6:

Different r2 threshold comparisons in regions associated with different chromatin states. Showing the comparison between two different r2 thresholds for the different chromatin states. Overall the odds ratios do not show significant differences.

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Additional file 7:

Correlation between ratio of odds ratios and CI width for significantly and suggestively trait-associated SNPs. Between the ratios of odds ratio and confidence interval width of significant and suggestive SNPs (r2 = 0.89; P-value = 1.60 × 10-26). The ratio can be a lot higher for suggestive SNPs, indicating that the confidence intervals are shorter. However, this may be due to a difference in the number of analyzed SNPs between the two datasets.

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Additional file 8:

Comparison of permutation results of significantly and suggestively trait-associated SNPs. That compares all permutation results for significantly and suggestively trait-associated SNPs.

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Additional file 9:

Histogram of distance to TSS for significantly trait-associated SNPs. Showing the distribution of distance to TSS across all significant and suggestive trait-associated SNPs and a close up of the <20 Kb region.

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Additional file 10:

Distance to TSS logistic regression graph. Showing the new β-coefficients of the genomic annotations in the logistic regression analysis.

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Additional file 11:

Table of distance to TSS log reg. Showing the estimated effect, standard error of the estimated effect, β-coefficient and the P-value of the genomic annotation included in the optimized model incorporating the distance to TSS variable.

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Additional file 12:

Table of changing odds ratios of select annotations before and after taking distance to TSS into account. Showing the changes in odds ratios of six different annotations before and after distance to TSS was included into a logistic regression model.

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Additional file 13:

Histogram of annotation overlaps for SNPs. Representing the percentage of SNPs (y-axis) overlapping with different numbers of annotations (x-axis) in all SNPs (grey) and the significantly trait-associated SNPs (black). A) Histogram of annotations identified to have a positive β-coefficient. For all SNPs: Mean: 1.89, Standard Deviation: 1.83. Trait-associated SNPs: Mean: 3.60, Standard Deviation: 2.26. B) Histogram of annotations identified to have a negative β-coefficient. For all SNPs: Mean: 0.54, Standard Deviation: 0.98. Trait-associated SNPs: Mean: 1.07, Standard Deviation: 0.78.

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Additional file 14:

Sources and description of genomic features. Containing a full description of all analyzed genomic features and their online sources.

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