Weighting sequence variants based on their annotation increases the power of genome-wide association studies in dairy cattle

Table 3 Enrichment of eight variant categories and their category-based significance thresholds

Category	Number of possible causal variants	Enrichment	Range of enrichment	Significance threshold
High impact	19	33.69	16.85–50.54	1.02e−7
Moderate impact	391	17.16	13.56–20.75	5.20e−8
Low impact	799	7.30	4.74–9.87	2.21e−8
3′ and 5′ UTR	343	16.64	12.56–20.43	5.04e−8
Open chromatin	7152	3.59	3.30–3.89	1.09e−8
Regulatory elements	9520	2.53	2.33–2.73	7.65e−9
Non-coding RNAs	95	22.70	15.27–30.12	6.88e−8
No known information	85,104	0.53	0.51–0.55	NA*

The confidence interval for each degree of enrichment is the 95% confidence interval obtained from bootstrapping resampled QTL 100 times
*Indicates that the category-based significance was not calculated for this annotation class since there was no enrichment for this category

ISSN: 1297-9686