The number of <i>cis-</i>regulated tags per gene.

<p>The percentages of cis-regulated tags mapping into the same gene are indicated (781 genes overall). For nearly half of the genes (48%) only one tag shows an eQTL effect. If multiple tags map within the same gene, only one eQTL tag should pass the FDR<0.05 significance threshold while the other tag could be less significant. For these eQTLs the allelic direction is shown: same allelic direction (multiple tags within the same gene are cis-regulated by a SNP in the same direction), significantly opposite allelic direction (multiple tags within the same gene are cis-regulated by a SNP but with opposite directions and the difference between the correlation coefficients is significant), or opposite allelic direction but not significant (if the difference between correlation coefficients is not significant).</p

<i>Cis-</i>regulating SNPs significantly^* affecting multiple tags of the same gene in opposite directions.

*<p>Only significant eQTLs with FDR<0.05 for both <i>cis-</i>regulated tags were used.</p

Trait-associated SNPs detected in the sequencing-based transcript-wise meta-analysis, but not detected in array-based eQTL dataset of 1,469 peripheral blood samples.

<p>Trait-associated SNPs detected in the sequencing-based transcript-wise meta-analysis, but not detected in array-based eQTL dataset of 1,469 peripheral blood samples.</p

The choice of proximal/distal polyadenylation site in genes <i>IRF5</i> and <i>HPS1</i> depends on the genotypes of rs10488630 and rs11189600, respectively.

<p>The ratio between the abundance of transcripts with proximal and distal 3′-UTR RT-qPCR products in <i>IRF5</i> (left) and <i>HPS1</i> (right) depends on the genotypes of <i>cis-</i>regulating SNPs rs10488630 and rs11189600, respectively. N denotes the number of individuals included in the analysis. These results indicate allele-specific preference for use of a proximal and distal polyadenlyation site.</p

Description of RNA next generation sequencing datasets.

<p>Description of RNA next generation sequencing datasets.</p

Fraction of <i>cis-</i>regulated genes in bins by mean gene expression levels for DeepSAGE and Affymetrix data.

<p>For each dataset, all genes were sorted by their mean gene expression levels, and divided into ten equal bins. The X-axis reflects these bins, which are sorted by increasing mean gene expression levels. The Y-axis reflects the fraction of <i>cis</i>-regulated genes that fall into each bin.</p

Number of <i>cis-</i>regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQTL mapping.

<p>Number of <i>cis-</i>regulated tags mapping to different genomic regions in tag-wise DeepSAGE eQTL mapping.</p

Trait-associated SNPs affecting DeepSAGE tags of 94 peripheral blood samples, but not detected in an array-based eQTL dataset of 1,469 peripheral blood samples.

<p>Trait-associated SNPs affecting DeepSAGE tags of 94 peripheral blood samples, but not detected in an array-based eQTL dataset of 1,469 peripheral blood samples.</p

Number of detected <i>cis-</i>eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.

<p>Number of detected <i>cis-</i>eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.</p

rs12934747*T creates a poly(A) signal in <i>LPCAT2</i> and leads to alternative polyadenylation site usage.

<p>The y-axis represents the number of counts for the deepSAGE tags. Two samples with different genotypes for SNP rs12934747, CC (reference allele) and TT (alternative allele), are shown as different traces. Below the coverage tracks, the position of rs12934747 is shown, together with the position of all reported polyadenylation sites from polyA_DB. An enlargement of the region containing the SNP is shown below. rs12934747 is located at the beginning of the 3′-untranslated region (3′-UTR) of <i>LPCAT2</i>, 27 nucleotides upstream a reported and experimentally validated polyadenylation site. This SNP changes the sequence, creating a polyadenylation signal that leads to the usage of the reported polyadenylation site. The square block indicates the sequence of the polyadenylation signal created by rs12934747. The creation of this signal shortens the 3′-UTR, as indicated by the higher abundance of the proximal DeepSAGE just upstream of the polyadenylation signal, and the nearly absent distal DeepSAGE, in the sample with the TT genotype (both tags indicated by arrows). Tag 2 was filtered out because it was expressed in less than 90% of individuals. There is an additional tag 3 in-between the proximal and distal tags, which is not <i>cis</i>-regulated.</p