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

BMC Genomics

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

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

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).

ISSN: 1471-2164