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Table 4 Regions of the genome with excess African ancestry in TB cases relative to controls

From: Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population

Length Mean African ancestry  
Region Begin-end SNP (Nr SNPs) TB cases Control Genes
5q11 rs26090-rs1382907 739064 (70) 0.6480 0.4615 ISL1
10q22 rs827299-rs7083934 6243529 (693) 0.6607 0.5030 UNC5B, SLC29A3, CDH23, C10orf105, PSAP, B7-H5, CHST3, SPOCK2, ASCC1, DDIT4, DNAJB12, MICU1, MCU, OIT3, PLA2G12B, P4HA1, NUDT13, FAM149B1, DNAJC9, MRPS16, TTC18, ANXA7, PPP3CB, MSS51, MYOZ1, AGAP5, SYNPO2L, CAMK2G, NDST2, SEC24C, ZSWIM8, FUT11, CHCHD1, PLAU, C10orf55, VCL, AP3M1, ADK, KAT6B, DUPD1, SAMD8, DUSP13, VDAC2, COMTD1, ZNF503
15q15 rs1712435-rs16966424 2669916 (182) 0.6511 0.4963 PLA2G4D, VPS39, GANC, TMEM87A, CAPN3, SNAP23, ZNF106, HAUS2, LRRC57, TTBK2, CDAN1, UBR1, EPB42, TMEM62, TGM5, TGM7, TP53BP1, LCMT2, ZSCAN29, TUBGCP4, ADAL, CKMT1B, MAP1A, PPIP5K1, STRC, CKMT1A, CATSPER2, PDIA3, MFAP1, SERF2, HYPK, ELL3, SERINC4, WDR76, FRMD5, CASC4, CTDSPL2, EIF3J, SPG11, PATL2
17q22 rs7210845-rs9908090 5200677 (479) 0.6579 0.4698 ANKFN1, NOG, C17orf67, TRIM25, DGKE, COIL, SCPEP1, AKAP1, MSI2, CCDC182, MRPS23, CUEDC1, SRSF1, VEZF1, DYNLL2, EPX, OR4D1, MKS1, OR4D2, LPO, MPO, BZRAP1, SUPT4H1, RNF43, HSF5, SEPT4, MTMR4, C17orf47, TEX14, RAD51C, PPM1E, TRIM37, SKA2, GDPD1, SMG8, PRR11, CLTC, DHX40, PTRH2, VMP1, RPS6KB1, TUBD1, RNFT1, HEATR6, CA4, USP32, SCARNA20, RPL32P32, C17orf64, APPBP2, PPM1D
  1. This table summarizes regions of the genome with excess African ancestry (San or Bantu), found in TB cases relative to controls, after adjusting for age, gender and genome-wide African ancestry. Ancestry segments that are associated with increased African ancestry in cases compared to controls were identified and contiguous segments were merged. P-values for each of the individual ancestry segments are available in Additional file 1: Table S2. The mean RFMix genome-wide African ancestry estimates are 0.6096 and 0.5238 for cases and controls respectively, and the standard deviation of local ancestry deviations is 0.0187 and 0.0336 in cases and controls respectively. Only regions of 500 000 base pairs or longer and that contain protein coding genes are shown (one short region on chromosome 5, one short region on chromosome 6, and four short regions on chromosome 10 were excluded).