Readme Summary of Supplemental Materials AF1: Binary CWD (0/1) EMMAX GWAS with no fixed-effect covariates and pseudo-lambda estimates. AF2: PP-Plot from AF1 EMMAX GWAS with no fixed-effect covariates. AF3: Binary CWD (0/1) EMMAX GWAS with Sex, Age, General U.S. Region as covariates and pseudo-lambda estimates. AF4: PP-Plot from AF3 EMMAX GWAS with Sex, Age, General U.S. Region as covariates. AF5: Binary CWD (0/1) EMMAX GWAS with Sex, Age, Farm (Farms with > 10 deer represented) as covariates and pseudo-lambda estimates. AF6: PP-Plot from AF5 EMMAX GWAS with Sex, Age, Farm (Farms with > 10 deer represented) as covariates. AF7: Supplemental Figure 1: (a) EMMAX GWAA for CWD with sex, age and U.S. region of origin as fixed effect covariates. (b) EMMAX GWAA for CWD with sex, age, and farm as fixed effect covariates. AF8: Binary CWD (0/1) EMMAX GxE (General U.S. Region as Interaction Term) GWAS with no fixed-effect covariates and pseudo-lambda estimates. AF9: PP-Plot from AF8 EMMAX GxE GWAS with no fixed-effect covariates. AF10: Binary CWD (0/1) EMMAX GxE (General U.S. Region as Interaction Term) GWAS with Sex, Age as fixed-effect covariates and pseudo-lambda estimates. AF11: PP-Plot from AF10 EMMAX GxE GWAS with Sex, Age as fixed-effect covariates. AF12: Supplemental Figure 2: Binary CWD (0/1) EMMAX GxE (General Region as Interaction Term) GWAS with Sex, Age as fixed-effect covariates. AF13: Binary CWD (0/1) Region Specific EMMAX GWAS (Northeast n = 286) with no fixed-effect covariates and pseudo-lambda estimates. AF14: Binary CWD (0/1) Region Specific EMMAX GWAS (Midwest n = 322) with no fixed-effect covariates and pseudo-lambda estimates. AF15: Binary CWD (0/1) Region Specific EMMAX GWAS (South n = 562) with no fixed-effect covariates and pseudo-lambda estimates. AF16: Binary CWD (0/1) Region Specific EMMAX GWAS (Northeast n = 286) with Sex, Age as fixed-effect covariates and pseudo-lambda estimates. AF17: Binary CWD (0/1) Region Specific EMMAX GWAS (Northeast n = 286) with Sex, Age, Farm as fixed-effect covariates and pseudo-lambda estimates. AF17-2: Binary CWD (0/1) Region Specific EMMAX GWAS (Northeast n = 286) with Sex, Age, Farm (Farm 5 Not Bifurcated) as fixed-effect covariates and pseudo-lambda estimates. AF18: Binary CWD (0/1) Region Specific EMMAX GWAS (Midwest n = 322) with Sex, Age as fixed-effect covariates and pseudo-lambda estimates. AF19: Binary CWD (0/1) Region Specific EMMAX GWAS (Midwest n = 322) with Sex, Age, Farm as fixed-effect covariates and pseudo-lambda estimates. AF20: Binary CWD (0/1) Region Specific EMMAX GWAS (South n = 562) with Sex, Age as covariates and pseudo-lambda estimates. AF21: Binary CWD (0/1) Region Specific EMMAX GWAS (South n = 562) with Sex, Age, Farm as fixed-effect covariates and pseudo-lambda estimates. AF22: Binary CWD (0/1) METAL Meta-Analysis with no fixed effect covariates and shared main effects across General U.S. Regions (Northeast, Midwest, South) and Cochran's Q with P-values for indentifying SNPs with regional heterogeneity of effects. AF23: PP-Plot for Cochran's Q P-values from AF22 METAL Meta-Analysis with no fixed-effect covariates. AF24: PP-Plot for Main Effect P-values from AF22 METAL Meta-Analysis with no fixed-effect covariates. AF25: Binary CWD (0/1) METAL Meta-Analysis with Sex, Age as fixed effect covariates and shared main effects across General U.S. Regions (Northeast, Midwest, South) and Cochran's Q with P-values for indentifying SNPs with regional heterogeneity of effects. AF26: PP-Plot for Cochran's Q P-values from AF25 METAL Meta-Analysis with Sex, Age as fixed-effect covariates. AF27: PP-Plot for Main Effect P-values from AF25 METAL Meta-Analysis with Sex, Age as fixed-effect covariates. AF28: Binary CWD (0/1) METAL Meta-Analysis with Sex, Age, Farm as fixed effect covariates and shared main effects across General U.S. Regions (Northeast, Midwest, South) and Cochran's Q with P-values for indentifying SNPs with regional heterogeneity of effects. AF29: PP-Plot for Cochran's Q P-values from AF28 METAL Meta-Analysis with Sex, Age, Farm as fixed-effect covariates. AF30: PP-Plot for Main Effect P-values from AF28 METAL Meta-Analysis with Sex, Age, Farm as fixed-effect covariates. TableS1:Summary of CWD Farm Prevalence For Farms Represented in the Present Study. TableS2:Summary of Significant SNPs from all EMMAX GWAS models and METAL Meta-Analyses. WTD_MetaData_Phenos: Excel Sheet of Deer Metadata including Deer ID (CMSID), Farm (Region_Farm), General U.S. Region of Origin (GeneralRegion_USA), Sex (0 = Male, 1 = Female), Age (in Years), CWD IHC Status (0 = nondetect, 1 = CWD Positive). MarkerMap: Tab Delimited Text File of SNP Marker Map with Chromosome and Position. 286_Northeast_WTD_GWAA_ForMETAL: Tab Delimited Text File with Deer ID (CMSID), Sex (0 = Male, 1 = Female), and CWD Binary IHC Status (Binary 0 = nondetect, 1 = CWD Positive) in columns 1-3, respectively, followed by SNPID's and numeric genotypes in all subsequent columns for n = 286 Northeast deer. 322_Midwest_WTD_GWAA_ForMETAL: Tab Delimited Text File with Deer ID (CMSID), Sex (0 = Male, 1 = Female), and CWD Binary IHC Status (Binary 0 = nondetect, 1 = CWD Positive) in columns 1-3, respectively, followed by SNPID's and numeric genotypes in all subsequent columns for n = 322 Midwest deer. 562_South_WTD_GWAA_ForMETAL: Tab Delimited Text File with Deer ID (CMSID), Sex (0 = Male, 1 = Female), and CWD Binary IHC Status (Binary 0 = nondetect, 1 = CWD Positive) in columns 1-3, respectively, followed by SNPID's and numeric genotypes in all subsequent columns for n = 562 South deer. 1170_WTD_GWAAs_IncludingGxE: Tab Delimited Text File with Deer ID (CMSID), General U.S. Region (GeneralRegion = South, Midwest, East = Northeast), Sex (0 = Male, 1 = Female), and CWD Binary IHC Status (Binary 0 = nondetect, 1 = CWD Positive) in columns 1-4, respectively, followed by SNPID's and numeric genotypes in all subsequent columns for n = 1170 deer (All General U.S. Regions Combined).