The motifs identified in TRIM haDHSs

Using the FIMO software to identified the putative transcription binding site motifs in TRIM haDHSs. And the corresponding six-primates sequences of these motifs were downloaed from Ensembl

Selection analysis of TRIM DHS

The TRIM DHS data was generated from 145 cell types DHS data in ENCODE. And the methodology of DHS selection analysis was based on our previous DHS research(Comprehensive identification and analysis of human accelerated regulatory DNA, Rachel et al.Genome Research)

Transposable elements within TRIM DHS

This files showed the transposable elements that overlapped with TRIM haDHSs and conversed DHSs and their detailed information. The first three columns represented the position of DHS, the fourth to sixth columns represented the position of transposable elements. The annotation file of transposable elements came from ReapeatsMasker output file in UCSC

Overview of study design.

<p>Abbreviations: ALI, acute lung injury; eQTL, eQTL, expression quantitative trait loci.</p

Manhattan plot of −log₁₀(p-value) for SNP association with ALI.

<p>Manhattan plot of −log₁₀(p-value) for SNP association with ALI.</p

Replicated SNPS with putative functional roles in ALI pathogenesis.

<p><b>Abbreviations:</b> Chr, chromosome; SNP, single nucleotide polymorphism; OR, odds ratio; Disc. or, odds ratio from phase 1 additive trend model; Disc. p, p value from phase 1 additive trend model; maf, minor allele frequency; ali: acute lung injury; repl. or, or from phase 2 additive trend model; repl. p, p value from phase 2 additive trend model.</p

Replicated SNP that alters expression in stimulated B-lymphoblastic cell lines (B-LCLs) [33].

<p><b>Abbreviations:</b> SNP, single nucleotide polymorphisms; Chr, chromosome; MAF, minor allele frequency; OR, odds ratio; mRNA, messenger ribonucleic acid; eQTL, expression quantitative trait loci.</p

ALI association of previously reported ALI candidate genes at the SNP and gene level in the discovery/Phase I population.

<p>SNP-level results are provided if the specific locus previously reported to associate with ALI was either directly genotyped by the Human 660quad platform or was able to be imputed with a posterior probability (r²) 0.90. If no imputation was possible due to SNP rarity or lack of linkage disequilibrium with genotyped markers, the result is given as “Not Available” (N/A). At the gene level, the strongest association reported for the gene, as annotated by the NCBI RefSeq position, is reported when associations resulted in a probability <i>p</i>≤0.01. If no SNP annotated to the gene was associated with <i>p</i>≤0.01, the result is given as “Not Significant” (NS). The results for <i>ANGPT2</i> in this population have previously been published <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028268#pone.0028268-Meyer1" target="_blank">[78]</a>.</p

Demographics of Trauma ALI SNP Consortium (TASC) subjects.

<p><b>Abbreviations:</b> ALI, acute lung injury; SNP, single nucleotide polymorphism; ISS, Injury Severity Score; NA, not applicable.</p

Quantile-Quantile (Q-Q) plot of single SNP association with ALI.

<p>Quantile-Quantile (Q-Q) plot of single SNP association with ALI.</p