Association results for chromosome 27.

<p><b>(A)</b> Chromosome 27 with association results colour-coded according to pair-wise LD (r²) with the top two SNPs (index 1 = chr27:745,156 bp and 2 = chr27:7,706,463 bp). <b>(B)</b> Minor allele frequency plot over chromosome 27. <b>(C)</b> Association results for the merged and imputed GWAS and sequence candidate SNPs dataset at the 0.7 Mb peak. The top SNP (chr27:735,281 bp) is located 418 bp upstream of <i>LACRT</i>, SNP position indicated by red arrow. Gene annotations are lifted over from the human genome. <b>(D)</b> Association results for the 7.7 Mb region. The top SNP (chr27:7,706,463 bp) is potentially located in an intron of <i>SLC38A4</i>.</p

Top ten GWAS regions defined by linkage disequilibrium (cut-off p<0.1 and r²>0.2).

<p>Top ten GWAS regions defined by linkage disequilibrium (cut-off p<0.1 and r²>0.2).</p

Haplotypes in the chromosome 11 candidate region.

<p><b>(A)</b> Phylogenetic tree displaying haplotype relationship of 15 SNPs in the candidate region on chromosome 11. The 51 haplotypes can be formed into three groups based on the tree clusters (separated by dashed lines). <b>(B)</b> Case/control frequencies in the three haplotype groups in the ESS cohort. There is a lower proportion of cases in haplotype group 1 compared to group 3.</p

Genome-wide association results.

<p><b>(A)</b> Quantile-quantile plot displaying a lambda of 1.00, indicating no residual inflation. Thin lines indicate 95% CI. SNPs with -log₁₀(p) values > 4 deviates from the expected distribution and are associated with CMT. <b>(B)</b> Manhattan plot displaying the results from the GWAS based on the Swedish ESS Illumina 170K genotypes. Genome-wide significance is reached for one SNP on chromosome 11 (73,290,522 bp) and nominal association is reached for seven SNPs on chromosomes 11 and 27.</p

SNPs associated with CMT.

<p>SNPs associated with CMT.</p

Multiple dimensional scaling plot visualising the genetic similarity between the individuals within the population using the two first principal components as calculated in PLINK.

<p>a) American and European data combined b) American data c) European data.</p

Manhattan plot showing the–log 10 p-values in relation to the chromosomes.

<p>a) American data b) European data c) American and European data combined. Q-Q plots showing the expected p-value in relation to the observed p-value for each GWAS analysis. Shaded area indicates 95% confidence interval. Stippled line marks nominal significance threshold.</p

a) Close up view of the most associated region from the American GWAS analysis. b) Minor allele frequency of the associated region. c) Further close up of the associated peak showing the LD structure of the SNPs in the area relative to the most associated SNP. d) Close up view of the genes located in the area of the associated haplotype.

<p>Red arrow indicates the location of the most associated SNP.</p