In this paper, we do not consider heritability of very rare SNPs. If stratified LD score regression were to be used to analyze a dataset with rare variants, then there would be several issues to consider that did not come up in our analysis. For example, in the current analysis, we could use LD estimates from a reference panel because the LD patterns in the reference panel matched the LD patterns in our samples for the allele frequency range we were interested in; this might not hold for rare variants [49]. Also, our analysis described above shows that allele-frequency dependent architectures are not causing bias in our current analyses, but this robustness result may not extend to potential future analyses of datasets with rare variants.
