Table 4. Variant annotations for 8,959,608 SNPs from FE dataset which is part of UKB.

Variant types selected for analysis are written in italics, and PTV burden components marked in bold. Some variants may have multiple effects. PTV - protein-truncating variants, UTR - untranslated region, TF - transcription factor, TFBS - transcription factor binding site.

Variant effect	Number of variants
intron_variant	3643472
missense_variant	2281322
synonymous_variant	1159078
splice_region_variant	333226
downstream_gene_variant	329399
upstream_gene_variant	303346
3_prime_UTR_variant	303346
5_prime_UTR_variant	192159
frameshift_variant	96359
intragenic_variant	85619
sequence_feature	79868
stop_gained	68054
structural_interaction_variant	57365
TF_binding_site_variant	45909
5_prime_UTR_premature_start_codon_gain_variant	34381
splice_donor_variant	22476
disruptive_inframe_deletion	21392
splice_acceptor_variant	18591
conservative_inframe_deletion	12612
disruptive_inframe_insertion	11080
intergenic_region	11012
conservative_inframe_insertion	8665
start_lost	5807
stop_lost	2442
protein_protein_contact	1590
stop_retained_variant	1077
initiator_codon_variant	609
TFBS_ablation	180
bidirectional_gene_fusion	17
gene_fusion	7
exon_loss_variant	5
3_prime_UTR_truncation	3
non_canonical_start_codon	2