Table 6 Distribution (%) of functional annotations of variants within the CI of QTL regions identified in within-population GWAS, and in fixed-effects and z-score meta-analyses (MA)
From: Sequence-based GWAS meta-analyses for beef production traits
Functional annotation | Within-population GWAS | Fixed-effects MA | z-score MA | Total |
|---|---|---|---|---|
Intergenic_region | 55.0 | 63.0 | 61.0 | 57.8 |
Intron_variant | 30.3 | 24.2 | 25.2 | 28.1 |
Upstream_gene_variant | 6.6 | 5.5 | 6.0 | 6.3 |
Downstream_gene_variant | 6.1 | 5.6 | 5.7 | 5.9 |
Missense_variant | 0.53 | 0.68 | 0.69 | 0.59 |
3_prime_UTR_variant | 0.49 | 0.40 | 0.59 | 0.49 |
Synonymous_variant | 0.44 | 0.23 | 0.24 | 0.36 |
5_prime_UTR_variant | 0.22 | 0.27 | 0.30 | 0.25 |
Splice_region_variant and intron_variant | 0.079 | 0.040 | 0.015 | 0.060 |
Stop_gained | 0.053 | 0.101 | 0.136 | 0.077 |
Frameshift_variant | 0.045 | 0.050 | 0.075 | 0.051 |
Non_coding_transcript_exon_variant | 0.023 | 0.020 | 0.030 | 0.023 |
5_prime_UTR_premature_start_codon_gain_variant | 0.011 | 0.010 | 0.000 | 0.009 |
Splice_region_variant and synonymous_variant | 0.011 | 0.000 | 0.000 | 0.007 |
Stop_lost and splice_region_variant | 0.004 | 0.000 | 0.000 | 0.002 |
Gene_fusion | 0.000 | 0.000 | 0.015 | 0.002 |