Overview

The plots here are designed to allow browsing overall trends in the SNP heritability and intercepts results from LD Score regression of the Neale Lab GWAS. Individual phenotype results can be viewed in the browser.

All plots below are restricted to results with at least some confidence in the LDSR results, and report SNP heritability on the liabulit scale. See the Methods section for more information on our selection of GWAS phenotypes, confidence ratings for the LDSR results, and significance thresholds.

In addition to the plots below, additional visualizations are available for considering:

Previous plots from the Round 1 results can be found in the Archive section.


SNP Heritability

The average SNP hertiability estimate across all 4178 primary GWAS is 0.065 (median = 0.058). Average estimates increase when restricting to any confidence (mean = 0.078, median = 0.059) or high confidence (mean = 0.088, median = 0.062). Strong departure from the null hypothesis of \(h^2_g=0\) is observed across phenotypes, especially among high confidence results.

SNP Heritability Estimates


SNP Heritability p-values

Note: The displayed 95% confidence bands assume tests are independent across phenotypes and do not account for multiple testing across annotations.


p-values by Confidence

Note: The displayed 95% confidence bands assume tests are independent across phenotypes within confidence rating and do not account for multiple testing across annotations. Read more about the confidence ratings here.


LDSR Intercept

Relative GWAS confounding or LDSR model misspecification is limited across the phenotypes, with a median intercept ratio of NA. Intercepts remain statistically significant for many phenotypes, including many high confidence phenotypes. Outlier intercept values > 1.2 are observed for home and birth location, height, and certain biomarkers.

Ratio Estimates

Note: Ratio estimates restricted to phenotypes with mean \(\chi^2 > 1\). Clearer results are observed by restricting to high confidence results and/or higher effective sample size using the filter on the right. The LDSR ratio estimate is:

\[\frac{\text{intercept}-1}{\text{mean}(\chi^2)-1}\]


Intercept Estimates


Int. p-values

Note: The displayed 95% confidence bands assume tests are independent across phenotypes and do not account for multiple testing across annotations.


Int. p-values by Confidence

Note: The displayed 95% confidence bands assume tests are independent across phenotypes within confidence rating and do not account for multiple testing across annotations. Read more about the confidence ratings here.


SNP Heritablity vs. Intercept

Among medium and high confidence phenotypes, there’s a positive relationship between the \(h^2_g\) estimate and the intercept estimate. This trend may indicate some degree of model misspecification in the paritioned LDSR model. Sample size may also be a factor if \(h^2_g\) is biased at some sample sizes, but comparison of \(h^2_g\) to the intercept ratio shows a similar trend towards non-zero ratios where \(h^2_g\) is large.

Estimates

Note: Clearer results are observed by restricting to high confidence results, continuous variables, and/or higher effective sample size using the filter on the right. Colors indicate our confidence rating as described in the Methods section.


Z scores

Note: Colors indicate our confidence rating as described in the Methods section.


SNP Heritability vs. Ratio

Note: Ratio estimates restricted to phenotypes with mean \(\chi^2 > 1\). Clearer results are observed by restricting to high confidence results, continuous phenotypes, and/or higher effective sample sizes using the filter on the right. Colors indicate our confidence rating as described in the Methods section. The LDSR ratio estimate is:

\[\frac{\text{intercept}-1}{\text{mean}(\chi^2)-1}\]