Regulatory elements, e.g., enhancers and promoters, have been widely reported to be enriched for disease and complex trait heritability. We investigated how this enrichment varies with the age of the underlying genome sequence, the conservation of regulatory function across species, and the target gene of the regulatory element. We estimated heritability enrichment by applying stratified LD score regression to summary statistics from 41 independent diseases and complex traits (average N ¼ 320K) and meta-analyzing results across traits. Enrichment of human putative enhancers and promoters was larger in elements with older sequence age, assessed via alignment with other species irrespective of conserved functionality: putative enhancer elements with ancient sequence age (older than the split between marsupial and placental mammals) were 8.83 enriched (versus 2.53 for all putative enhancers; p ¼ 3eÀ14), and promoter elements with ancient sequence age were 13.53 enriched (versus 5.13 for all promoters; p ¼ 5eÀ16). Enrichment of human putative enhancers and promoters was also larger in elements whose regulatory function was conserved across species, e.g., human putative enhancers that were enhancers in R5 of 9 other mammals were 4.63 enriched (p ¼ 5eÀ12 versus all putative enhancers). Enrichment of human promoters was larger in promoters of loss-of-function intolerant genes: 12.03 enrichment (p ¼ 8eÀ15 versus all promoters). The mean value of several measures of negative selection within these genomic annotations mirrored all of these findings. Notably, the annotations with these excess heritability enrichments were jointly significant conditional on each other and on our baseline-LD model, which includes a broad set of coding, conserved, regulatory, and LD-related annotations.

Family history of disease can provide valuable information in case-control association studies, but it is currently unclear how to best combine case-control status and family history of disease. We developed an association method based on posterior mean genetic liabilities under a liability threshold model, conditional on case-control status and family history (LT-FH). Analyzing 12 diseases from the UK Biobank (average N =350K), we compared LT-FH to genome-wide association without using family history (GWAS) and a previous proxy-based method incorporating family history (GWAX). LT-FH was +63% (s.e. 6%) more powerful than GWAS and +36% (s.e. 4%) more powerful than the trait-specific maximum of GWAS and GWAX, based on the number of independent genome-wide significant loci across all diseases (e.g. 690 loci for LT-FH vs. 423 for GWAS); relative improvements were similar when applying BOLT-LMM to GWAS, GWAX, LT-FH phenotypes. Thus, LT-FH greatly increases association power when family history of disease is available.

Personal oral hygiene in the absence of fluorides has failed to show a benefit in terms of reducing the incidence of dental caries.