Schizophrenia association enrichment in eQTLs.

Q-Q and fold enrichment plots for adipose, epidermal, LCL and whole blood eQTLs. The baseline is determined by respectively matched control SNP sets. The fold enrichment is displayed in logarithmic scale.</p

Cross-tissue eQTLs in the loci with genome-wide significant association with schizophrenia.

Cross-tissue eQTLs in the loci with genome-wide significant association with schizophrenia.</p

Schizophrenia association enrichment of eQTLs with different Roadmap functional annotations.

Chi-squared general linear model coefficients for eQTLs of different tissues (adipose, epidermal, lymphoblastoid cell lines (LCL), whole blood) and location (proximal, distal) affiliated to different Roadmap functional elements. “All” stands for all eQTLs (* p p < 0.001).</p

Enrichment statistics and general linear model coefficients for squared schizophrenia association z-scores differences between adipose tissue, epidermal tissue, lymphoblastoid cell lines (LCL) and whole blood eQTLs, and matching control variants.

Enrichment statistics and general linear model coefficients for squared schizophrenia association z-scores differences between adipose tissue, epidermal tissue, lymphoblastoid cell lines (LCL) and whole blood eQTLs, and matching control variants.</p

Relationship between polygenicity and eQTL association enrichment across different GWASes.

Differences (Mann-Whitney test p-values) in association p-values between eQTLs and control variants of various types as functions of the estimated proportions of non-null associations. The GWAS names or acronyms are color-coded to represent different categories (azure = anthropometric [height]; red = cardiovascular, systolic blood pressure [SBP]; green = immune, rheumatoid arthritis [RA]; gold = metabolic, body mass index [BMI], type-II diabetes [T2D]; black = schizophrenia) and their sizes are proportional to the respective chi-squared linear model coefficients (* p p < 0.001).</p

Zoom plot for DEP and LDL centered on the variant rs174594, close to the Fatty Acid Desaturase 2 (<i>FADS2</i>) gene.

This leadSNP was in common for depression, HDL, LDL, TC and TG. (TIF)</p

Polygenic overlap between depression (DEP) sc-reactive protein (DEP)(DEP|CRP).

Conditional q-q plot of nominal versus empirical–log 10p values (corrected for inflation) in primary trait (DEP) below the standard GWAS threshold of p (TIF)</p

Polygenic overlap between depression (DEP) and systolic blood pressure (DEP)(DEP|SBP).

Conditional q-q plot of nominal versus empirical–log 10p values (corrected for inflation) in primary trait (DEP) below the standard GWAS threshold of p (TIF)</p

Polygenic overlap between low-density lipoprotein and depression (LDL) (LDL|DEP).

Conditional q-q plot of nominal versus empirical–log 10p values (corrected for inflation) in primary trait (LDL) below the standard GWAS threshold of p (TIF)</p

Mixer results for depression (DEP) and c-reactive protein (CRP).

(TIF)</p