pheno_id Start End Chromosome

pheno_id tissue_name variant_id rsid REF ALT start_distance af beta_g1 beta_se_g1 pval_g1 celltype_name
pheno_id tissue_name variant_id rsid REF ALT start_distance af beta_g1 beta_se_g1 pval_g1 celltype_name
pheno_id tissue_name variant_id rsid REF ALT start_distance af beta_g1 beta_se_g1 pval_g1 celltype_name
pheno_id tissue_name variant_id rsid REF ALT start_distance af beta_g1 beta_se_g1 pval_g1 celltype_name

Tissue Expression: Each box groups non-zero TPM records for the selected gene by tissue, combining records from its different cell types. Each value is plotted as log2(TPM + 1). Only outlying observations are shown as individual points; other observations contribute to the boxplot but are not shown separately. The center line is the median, the box spans the first to third quartiles (Q1–Q3), and the whiskers extend to the most extreme observations within 1.5 × the interquartile range. The number of records is not necessarily the number of independent biological samples.

Original bulk RNA-seq samples by tissue: Blood (1,515), Liver (1,347), Rumen (902), Uterus (883), Mammary Gland (830), Lung (593), Lymph Node (395), Testis (272), Jejunum (241), Placenta (205), Pituitary (198), Hypothalamus (178), Ileum (127), CNS (111), Epididymis (105), Skin (105), Colon (99), Large Intestine (72), Duodenum (56), Oviduct (46), Heart (43), and Spleen (41).

These are the total available samples per tissue before filtering for the selected gene. The boxplots exclude records with TPM = 0, so the observations included depend on the gene. Tissue-level plots also combine records across cell types; these tissue totals are not the number of observations in an individual box, nor are they sample counts for each tissue–cell-type group.

SNP rsid pheno_id tissue_name cs PIP ct ATAC_status Chromatin_state SNP_annotation
SNP rsid pheno_id tissue_name cs PIP ct ATAC_status Chromatin_state SNP_annotation

pheno_id tissue map_model variant_id rsid start_distance af beta_g1 beta_se_g1 pval_g1 snp_r celltype
pheno_id tissue map_model variant_id rsid start_distance af beta_g1 beta_se_g1 pval_g1 snp_r celltype

pheno_id tissue celltype traits res.summary
pheno_id tissue celltype traits res.summary
pheno_id tissue celltype traits res.summary
pheno_id tissue celltype traits res.summary
pheno_id variant_id rsid start_distance af beta_g1 beta_se_g1 pval_g1 SNP_PP_H4 trait_name tissue_name ATAC_status Chromatin_state Enrichment SNP_annotation
pheno_id variant_id rsid start_distance af beta_g1 beta_se_g1 pval_g1 SNP_PP_H4 trait_name tissue_name ATAC_status Chromatin_state Enrichment SNP_annotation
pheno_id variant_id rsid start_distance af beta_g1 beta_se_g1 pval_g1 SNP_PP_H4 trait_name tissue_name ATAC_status Chromatin_state Enrichment SNP_annotation

pheno_id gene_name gene_type alpha n_snps_in_window n_snps_in_model lambda_min_mse test_R2_avg test_R2_sd cv_R2_avg cv_R2_sd in_sample_R2 nested_cv_fisher_pval rho_avg rho_se rho_zscore rho_avg_squared zscore_pval cv_rho_avg cv_rho_se cv_rho_avg_squared cv_zscore_est cv_zscore_pval cv_pval_est
pheno_id gene_name zscore effect_size pvalue var_g pred_perf_r2 pred_perf_pval n_snps_used n_snps_in_cov n_snps_in_model best_gwas_p largest_weight tissue_celltype trait_name

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