Additional file 2 of A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits

Additional file 2: Table S1. Inflation factor (lambda) for each trait. The inflation of observed chi-squared statistic due to population structure was checked. Table S2. Annotation of pleiotropic effects on individual traits for 178 putative causal variants identified from the multi-trait conditional GWAS. The annotation includes positions, functional classification, rs ID where available and signed significant t-values (|t| > 1.96) were provided for 178 variants across the 16 traits at two ages. Gene names and distances from the nearest genes are also provided if variants are located in or within 100 kb of the gene. Table S3. Annotation of 1510 sequence variants in strong LD with the 178 most significant variants from multi-trait conditional GWAS. The annotation includes the positions, rs ID where available, functional classification and P values of multi-trait $$\chi ^{2}$$ χ 2 statistic. The names of the nearest genes are also provided if variants are located in or within 100 kb of the gene. Table S4. List of 453 published genes previously associated with fibre characteristics in mammals (“Published-Gene set”) used to identify sequence variants to be includes in BayesR and GBLUP analysis. Ensembl identification, name of genes and gene location (chromosome number, start and end position in bp).