Counts and proportions of gene structure-based categories and protein consequences in local SNPs and cis-eQTLs.

Local SNPs and cis-eQTLs that affect mRNA transcripts are counted within each gene-based functional category (upper panel) and for each protein consequence (lower panel).Enrich: the fold change in proportion that each group constitutes among cis-eQTLs compared to among all local SNPs.The category “Exonic” does not include 5′ and 3′ untranslated regions (UTRs); “Upstream” and “Downstream” each includes regions within 1 kb from transcription start or end sites of genes, respectively; “Splicing” includes SNPs 2 bp from exon-intron splicing junctions and within an intron; SNPs 2 bp from a splice junction and within an exon are designated “Exonic”); “Intronic” includes SNPs in introns, but not those 2 bp from exon-intron splicing junctions; “nonsyn” indicates a SNP in an Exonic that is non-synonymous; “syn” indicates an SNP in an Exonic that is synonymous; “stopgain” indicates an SNP in an Exonic and with a variant that causes the creation of stop codon; “stoploss” indicates an SNP in an Exonic and with a variant that eliminates a stop codon.N.A. means “Not Available” and includes SNPs that were found in a gene, but that could not be assigned to a specific functional category.Totals for gene-structure-based classification and protein consequences are shown in bold font.