Table 2 Enriched heritability by functional, cellular, and candidate gene-set annotations. prSNPs refers to proportion of SNPs in the model, prH2 refers to proportion on the heritability (SE) attributed to the annotation set, and enrichment refers to the enrichment (SE; P value) in heritability given the number of SNPs in the model

Function: weak enhancer +/−500 bp

0.299 (0.06)

2.82 (0.61); P = 0.0045

Function: conserved

0.258 (0.08)

4.94 (1.46); P = 0.0047

Cell: CNS: mid-frontal lobe: H3k27ac

0.132 (0.04)

4.89 (1.34); P = 0.0056

Function: enhancer +/−500 bp

0.402 (0.08)

2.24 (0.44); P = 0.0065

Function: DNASE I hypersensitivity site (foetal) +/−500 bp

0.666 (0.11)

1.84 (0.32); P = 0.0099

Candidate: Mendelian disease [11] genes

0.040 (0.01)

2.19 (0.49); P = 0.0132

Candidate: PGC schizophrenia GWAS loci [19]

0.035 (0.01)

2.50 (0.70); P = 0.0211

Function: H3k4me1

0.771 (0.10)

1.43 (0.19); P = 0.0303

Function: CCCTC-binding factor

0.129 (0.05)

4.71 (1.75); P = 0.0326

Cell: CNS: hippocampus middle: H3k4me1

0.211 (0.06)

2.76 (0.81); P = 0.0351

Cell: CNS: angular gyrus: H3k27ac

0.106 (0.03)

3.25 (1.03); P = 0.0365

Function: digital genomic footprint +/−500 bp

0.836 (0.10)

1.35 (0.17); P = 0.0399

Function: conserved +/−500 bp

0.603 (0.07)

1.34 (0.17); P = 0.0488