Includes Supplementary Figures S1-S13, Supplementary Tables S1-S8 and Supplementary Methods. Suppl. Fig. S1: Principal component analysis of the new populations genotyped from the Sudanese region; Suppl. Fig. S2: Principal component analysis of six world–wide populations from 1000 Genomes Project using different number of SNPs; Suppl. Fig. S3: Principal component analysis of the new populations genotyped from the Sudanese region; Suppl. Fig. S4: Principal component analysis of the populations from the Sudanese region in the context of the African continent with 14 samples identified as outliers with respect to their populations of origin; Suppl. Fig. S5: Pairwise FST values between the 14 populations; Suppl. Fig. S6: Cross-validation error estimates of the new nine genotyped populations for the ADMIXTURE analysis; Suppl. Fig. S7: ADMIXTURE results for k = 2 through k = 10 for the Sudanese populations; Suppl. Fig. S8: Cross-validation error estimates of the 14 populations for the ADMIXTURE analysis; Suppl. Fig. S9: ADMIXTURE results for k = 2 through k = 10 for the 14 populations using all 921 individuals; Suppl. Fig. S10: ADMIXTURE results for k = 2 through k = 10 for populations from the Sudanese region in the context of other external populations; Suppl. Fig. S11: Principal component analysis of the populations from the Sudanese region in the context of the African continent with an European population added; Suppl. Fig. S12: ADMIXTURE results for k = 2 through k = 10 for populations from the Sudanese region in the context of other external populations; Suppl. Fig. S13: Sampling distribution of the sample mean Global FST between Sudanese populations. Suppl. Table S1: Detailed sample information of the populations analysed in the present study, including sampling location and total number of individuals; Suppl. Table S2: Pairwise FST comparisons among the Sudanese ethnolinguistic groups and neighbouring populations; Suppl. Table S3: Three–population test with Yoruba as outgroup to estimate mixing proportions; Suppl. Table S4: Three–population test with Luya as outgroup to estimate mixing proportions; Suppl. Table S5: List of genes related to resistance to malaria present in the Immunochip; Suppl. Table S6: List of genes belonging to pathways related to antibacterial host defence present in the Immunochip; Suppl. Table S7: List of genes belonging to fungi host defence present in the Immunochip; Suppl. Table S8: Summary statistics of SNPs of disease-related genes from African populations of 1000 Genomes Project compared to the portion of those SNPs genotyped in the Immunochip. The compressed file contains the Sudan Inmunochip dataset in XLSX, BED, BIM and FAM formats.