NAHR deletion rate at the <i>CMT1A</i> locus in MZ co-twins.

<p>The estimates of deletion rate for each co-twin are plotted against one another, with 95% confidence intervals for each estimate also shown.</p

NAHR deletion rate at the <i>CMT1A</i> locus in all the sperm samples analysed with men grouped according to <i>PRDM9</i> zinc finger motif-binding status.

<p>Men homozygous for alleles recognising the canonical motif (shown in red) or heterozygous for alleles recognising the canonical and non-canonical motifs (shown in blue) are grouped separately and shown in ascending order. The 95% confidence intervals for each estimate of deletion rate are shown.</p

NAHR deletion rate at the <i>CMT1A</i> locus plotted against age at the time the sample was provided.

<p>In cases where multiple individuals have the same age the points are plotted slightly offset from each other on the x-axis. The 95% confidence intervals for each estimate of deletion rate are shown.</p

Participant characteristics (Primary Study).

<p>Values are means ± standard deviation for each quantitative trait.</p

Patterns of CpG Methylation in abdominal SAT. A:

<p>DMH data show a bimodal pattern consistent with hypo- and hypermethylation. <b>B:</b> CpG sites close to TSS’s on the X chromosome are hemimethylated in females. <b>C:</b> CpG sites close to TSS’s of Imprinted Genes are hemimethylated <b>D:</b> Lower methylation is observed around TSS’s (black line shows 300 bp sliding window median methylation score).</p

Replicated meQTL hits.

<p>a) ID of probe set on DMH array,</p><p>b) chromosome.</p><p>c) genomic coordinates of probe set in build37.</p><p>d) genomic coordinates of SNP in build37.</p><p>e) coefficient of SNP effect.</p><p>f) standard error for the SNP effect.</p><p>g) p-value for the SNP effect.</p><p>h) ID of probe on Illumina 27k array,</p><p>i) genomic coordinates of CpG probed in build37.</p><p>j) one-sided p-value for the SNP effect in the direction of the original association.</p

Genome-wide meQTL analysis. A:

<p><i>Cis</i>-meQTL quantile-quantile plot showing enrichment of association signal. Grey bands correspond to 95% confidence intervals. <b>B:</b> Significant meQTL are located close to CpG sites.</p

–log₁₀<i>P</i> values of the 5 replicated meQTLs against genomic position, with the top SNP indexed and indicated by a diamond.

<p>Estimated recombination rates are shown in blue, and SNP LD is given by colour as shown in the legends (LD data from 1000 Genomes Nov 2010 CEU genotypes).</p

Participant characteristics (Replication Study).

<p>Values are means ± standard deviation for each quantitative trait.</p

Flowchart showing the analysis pipeline.

<p><b>Top:</b> Association of DMH Methylation Score with phenotypes. <b>Bottom:</b> Primary <i>cis</i>-meQTL association study, followed by replication study. <b>Left:</b> Association of DMH probe sets with significant meQTLs with mRNA expression. <b>Right:</b> Text mining of meQTLs significant in the primary study.</p