for the focal annotation in this regression represents a positive contribution of this annotation to trait heritability, conditional on the other annotations. We report regression coefficients, normalized by mean per-SNP heritability, together with a P-value to test whether the regression coefficient is significantly positive. Stratified LD score regression requires GWAS summary statistics for the trait of interest, together with an LD reference panel (e.g. 1000 Genomes22), and has been shown to produce robust results with properly controlled type I error7. We have released open source software implementing our approach, and have also released all genome annotations derived from the publicly available gene expression data that we analyzed (see URLs). We call our approach LD score regression applied to specifically expressed genes (LDSC-SEG).
