Disease associated SNPs (candSNPs) and coding variant SNPs (cSNPs).

<p>Disease associated SNPs (candSNPs) and coding variant SNPs (cSNPs).</p

Results of Association Studies.

*<p>MAF – minor allele frequency.</p>**<p>number of subjects included in the analysis.</p>***<p>p-value>0.05.</p

List of genes.

<p>List of genes.</p

Association results of maternal traits in the HAPO cohort.

<p>Blue diamonds correspond to association results for SNPs in the complete cohort (All). The red squares correspond to association results for SNPs in the European ancestry cohort (Eur_Anc). The green triangles correspond to association results for SNPs in the Thai cohort (Thai). The -log₁₀p-value for each association test is shown along the y-axis, and the location of each SNP is indicated along the x-axis. The genomic region included in the genetic analysis is illustrated below each panel of association results (based on USC genome browser May 2004 (NCBI35/hg17) build). FPG = fasting plasma glucose levels during OGTT; All n = 5546, European Ancestry n = 3834, and Thai n = 1712. 1-hour PG = 1-hour plasma glucose levels during OGTT; All n = 5543, European Ancestry n = 3833, and Thai n = 1710. 1-hour CP = 1-hour c-peptide during OGTT; All n = 5549, European Ancestry n = 3836, and Thai n = 1713. HbA1c; All n = 5216, European Ancestry n = 3648, and Thai n = 1568.</p

Baseline characteristics of study participants.

<p>Baseline characteristics of study participants.</p

Candidate gene characteristics.

*<p>htSNPs = Haplotype tagged SNPs.</p

LocusZoom plot of chronotype associations in the <i>PER2</i> locus.

<p>Variants are coloured by their LD r² with lead variant rs75804782 and those with association <i>P</i>-values > 0.01 were omitted for clarity.</p

LocusZoom plots of sleep duration associations in the <i>VRK2</i> locus.

<p>Both plots show the same locus but each highlights a different lead variant: rs1380703 (left) and rs17190618 (right). Variants with association <i>P</i>-values > 0.01 were omitted for clarity. The two leads variants represent separate signals.</p

Genetic variants associated with chronotype (as either a continuous or binary trait) at <i>P</i><5x10^-8 in the UK Biobank study.

<p>Variants highlighted in bold were not identified by the 23andMe study, those in italic did not reach genome-wide significance on meta-analysis and those not highlighted replicate previously reported loci from 23andMe. Genes listed are candidate or nearest genes within 250Kb of the lead SNP. Odds ratios correspond to risk of morningness over eveningness. Beta, OR and frequency refers to A1. Replication data is based on continuous data and as the replication beta is in different units to the discovery GWAS beta, a P-value meta-analysis was performed.</p

Manhattan and quantile-quantile (QQ) plots for chronotype.

<p>Summary information plots for inverse-normalised (self-report) Sleep Duration vs. ~16.8 million imputed genetic variants in 127,573 White British individuals in the UK Biobank study. The Manhattan plot (top) shows association test (-log₁₀ <i>P</i>-value on the y-axis against physical autosomal location on the x-axis with the standard genome-wide significance cutoff of <i>P</i> = 5x10^-8 shown by the horizontal black line. Variants tested had imputation R²>0.4, a Hardy-Weinberg Equilibrium (HWE) <i>P</i>-value > 1x10^-6 and minor allele frequency (MAF) > 0.1%. The Sleep Duration QQ plot (bottom) identifies some inflation (λ_GC = 1.097) but, as with Chronotype, this is consistent with expected inflation from a highly polygenic trait in such a large sample size [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006125#pgen.1006125.ref015" target="_blank">15</a>].</p