Population-sense regional heritability for each brain-measured intermediate phenotype within the top g_f associated region on chromosome 5.

<p>²_ps: estimated regional population-sense heritability, SE: estimated standard error of the regional population-sense heritability. P:p-value from the LRT test testing the significance of the genetic variance component. Tissue: brain region, h</p

Distribution of population sense-heritability inside and outside genes.

<p>Distribution of heritability estimated from all SNPs, SNPs inside genes and SNPs outside genes by chromosome for crystallised intelligence, fluid intelligence and cognitive decline.</p

Variance explained for top ten regions ranked by significance or LRT for crystallised and fluid intelligence and cognitive decline.

<p>^a heritability of region when full model fitting 11 variance components first ten independent (i.e. non overlapping) regions and rest of genome.</p><p>^b Only the best supported of multiple overlapping regions was fitted.</p

Genome wide thresholds for the Likelihood Ratio Test (LRT) derived from N permutations.

<p>Genome wide thresholds for the Likelihood Ratio Test (LRT) derived from N permutations.</p

Plot of likelihood ratio test for phenotypic variance explained by each of 10,908 regions (groups of 101 consecutive SNPS) (bars) and −log₁₀ P-values>2.7 for single SNP association (circles).

<p>Dashed line is 1% nominal significance threshold for LRT for individual regions, dotted line is 5% genome-wide significance threshold for individual regions obtained by permutation analysis. <b>A</b> crystallised intelligence n = 1791, <b>B</b> fluid intelligence n = 1706 , and <b>C</b> cognitive change n = 1602.</p

Region on chromosome 5 significantly associated with fluid intelligence.

<p>Annotation from Ensembl genome browser.</p

Population-sense heritability (diagonal), phenotypic (upper diagonal) and genetic (lower diagonal) correlations for measures of general intelligence and cognitive decline estimated from relationship matrices based on 547,750 SNP genotypes.

<p> Heritabilities on diagonal, genetic correlations below diagonal, phenotypic correlations above diagonal and standard errors given in brackets.</p

Pleiotropic regions affecting multiple traits.

<p>Pleiotropic regions affecting multiple traits.</p

Distribution of the likelihood ratio test and variance explained under the null hypothesis.

<p>Comparison of the distribution of likelihood ratio test and variance explained for 5454 regions spanning 101 SNPs for fluid intelligence, crystallised intelligence and cognitive change. Lower set of distributions for each plot are from the real data, upper set are the 5% genome-wide significance threshold from each of 500 permuted data sets i.e. empirical null distribution.</p

Comparison of significance of region and top SNP within region.

<p>Scatter plot of −log₁₀ P-values for single SNP association of greatest significance in region and significance of LRT test for variance explained by entire region (each region contains 101 SNPs). Correlation coefficient is 0.52.</p