The SNV rate within the variant classification system is also stable (standard deviations < 0.004). On average, 0.55% of variants are Category 1, 1.48% Category 2, 1.16% Category 3, 4.44% Category 4, 17.96% Category 5, and 30.67% Category 6 (Fig. 2B; Supplemental Table S3). As expected, the significant enrichment of the rate of heterozygous and homozygous variants in RegulomeDB features is also evident in the enrichment of variants in the score categories of 2–6 (paired, two-tailed t-test; P < 5 × 10−15) (Supplemental Table S3). However, Category 1 variants show an opposite bias, likely due to the lack of rare variants in eQTL studies.
