Table 3 Tag-SNP haplotype scoring and tag efficiency in the CTLA4 gene in worldwide populations

From: Haplotype tagging efficiency in worldwide populations in CTLA4 gene

   Present tag-SNPs a Johnson's tag-SNPs b Present tag-SNPs b
Continental region Population Kh common (%)c Kdetected (%)d Tag efficiency Kh common (%)c Kdetected (%)d Tag efficiency Kdetected (%)d Tag efficiency
Sub-Saharan Bantu (BAN) 7 (80.00) 5 (84.38)   7 (95.00) 4 (73.68)   5 (84.21)  
Africa Biaka Pygmies (BPY) 6 (68.57) 4 (70.83)   6 (88.57) 4 (87.13)   4 (80.69)  
  Mandenka (MAN) 5 (63.64) 4 (89.31)   6 (93.18) 4 (60.94)   5 (82.94)  
  Mbuti Pygmies (MPY) 6 (70.00) 3 (61.86)   5 (93.33) 3 (75.04)   3 (78.57)  
  Tanzan (TAN) 3 (71.88) 3 (100.00)   5 (92.19) 4 (89.80)   4 (89.80)  
  Yoruba (YOR) 9 (89.47) 5 (67.48)   7 (100.00) 4 (73.70)   5 (76.30)  
  Mean 6.00 (73.93) 4.00 (78.98) 14.60 6.00 (93.71) 3.83 (76.71) 14.38 4.33 (82.09) 19.23
North-Africa Moroccan (MRA) 4 (71.43) 4 (100.00)   4 (82.86) 4 (100.00)   4 (100.00)  
  Mozabite (MOZ) 4 (65.00) 3 (92.31)   4 (86.67) 3 (92.27)   3 (92.27)  
  Saharaui (SAH) 4 (66.04) 4 (100.00)   5 (85.85) 5 (100.00)   4 (93.36)  
  Mean 4.00 (67.49) 3.67 (97.44) 21.92 4.33 (85.12) 4.00 (97.42) 16.58 3.67 (95.21) 27.01
Middle East Bedouin (BED) 5 (66.67) 3 (81.55)   5 (81.11) 5 (100.00)   2 (71.15)  
  Druze (DRU) 6 (62.22) 3 (55.32)   7 (92.22) 6 (90.35)   2 (43.29)  
  Palestinian (PAL) 5 (69.61) 3 (83.05)   6 (89.22) 6 (100.00)   2 (61.44)  
  Mean 5.33 (66.17) 3.00 (73.31) 24.25 6.00 (87.52) 5.67 (96.78) 16.94 2.00 (58.63) 51.31e
Europe Adygei (ADY) 8 (97.06) 4 (72.49)   7 (97.06) 6 (87.84)   5 (81.76)  
  Basque (BAS) 6 (78.05) 4 (84.37)   6 (90.24) 5 (91.91)   4 (82.49)  
  Catalan (CAT) 6 (80.00) 4 (87.50)   5 (92.50) 5 (100.00)   4 (94.59)  
  Continental Italian (CIT) 6 (77.27) 4 (79.42)   6 (90.91) 5 (92.52)   4 (82.51)  
  French (FRE) 3 (71.74) 3 (100.00)   5 (93.48) 5 (100.00)   3 (81.39)  
  French Basque (FRB) 4 (79.17) 3 (89.52)   4 (87.50) 4 (100.00)   3 (90.51)  
  Orcadian (ORC) 5 (96.88) 4 (93.50)   5 (100.00) 4 (93.70)   4 (93.70)  
  Russian (RUS) 3 (76.00) 3 (100.00)   3 (84.00) 3 (100.00)   3 (100.00)  
  Sardinian (SAR) 6 (79.63) 4 (85.93)   6 (96.30) 6 (100.00)   5 (82.66)  
  Spanish (SPA) 4 (66.20) 3 (90.48)   5 (78.17) 4 (90.15)   4 (90.15)  
  Mean 5.10 (80.20) 3.60 (88.32) 23.61 5.20 (91.02) 4.70 (95.61) 17.40 3.90 (87.98) 26.69
Central/South Asia Balochi (BAL) 4 (72.92) 3 (88.62)   3 (81.25) 3 (100.00)   3 (100.00)  
  Brahui (BRA) 4 (76.00) 2 (78.95)   4 (90.00) 4 (100.00)   3 (91.11)  
  Burusho (BUR) 3 (82.00) 3 (100.00)   4 (92.00) 4 (100.00)   3 (93.48)  
  Hazara (HAZ) 4 (87.50) 3 (88.11)   3 (91.67) 3 (100.00)   2 (88.65)  
  Kalash (KAL) 5 (90.00) 3 (82.22)   4 (96.00) 4 (100.00)   3 (91.67)  
  Makrani (MAK) 3 (77.27) 2 (91.20)   4 (93.18) 4 (100.00)   2 (85.40)  
  Pathan (PAT) 3 (83.33) 3 (100.00)   3 (93.75) 3 (100.00)   3 (100.00)  
  Sindhi (SIN) 4 (82.00) 3 (92.68)   5 (92.00) 4 (93.48)   3 (86.96)  
  Mean 3.75 (81.38) 2.75 (90.22) 36.71 3.75 (91.23) 3.63 (99.18) 18.10 2.75 (92.16) 42.04
East Asia Cambodian (CAM) 5 (90.91) 4 (85.04)   4 (95.45) 4 (100.00)   4 (100.00)  
  Han (HAN) 4 (86.67) 4 (100.00)   4 (98.89) 4 (100.00)   4 (100.00)  
  Japanese (JAP) 3 (78.57) 3 (100.00)   3 (91.07) 3 (100.00)   3 (100.00)  
  North China (NCH) 4 (86.03) 4 (100.00)   4 (97.79) 4 (100.00)   4 (100.00)  
  South China (SCH) 5 (77.86) 4 (92.68)   4 (87.86) 4 (100.00)   4 (100.00)  
  Yakut (YAK) 3 (74.00) 3 (100.00)   3 (94.00) 3 (100.00)   3 (100.00)  
  Mean 4.00 (82.34) 3.67 (96.29) 26.43 3.67 (94.18) 3.67 (100.00) 18.84 3.67 (100.00) 31.39
Oceania Nan Melanesian (NAN) 3 (83.33) 3 (100.00)   3 (90.48) 3 (100.00)   2 (86.85)  
  Papuan (PAP) 5 (90.00) 4 (92.56)   3 (93.33) 3 (100.00)   2 (82.11)  
  Mean 4.00 (86.67) 3.50 (96.28) 41.72 3.00 (91.90) 3.00 (100.00) 18.38 2.00 (84.48) 77.64e
America Colombian (COL) 3 (84.62) 3 (100.00)   3 (88.46) 3 (100.00)   3 (100.00)  
  Karitiana (KAR) 2 (95.65) 2 (100.00)   2 (95.65) 2 (100.00)   2 (100.00)  
  Maya (MAY) 3 (82.61) 3 (100.00)   3 (86.96) 3 (100.00)   3 (100.00)  
  Pima (PIM) 3 (89.13) 3 (100.00)   3 (91.30) 3 (100.00)   3 (100.00)  
  Surui (SUR) 2 (97.61) 2 (100.00)   2 (97.62) 2 (100.00)   2 (100.00)  
  Mean 2.60 (89.93) 2.60 (100.00) 44.97 2.60 (92.00) 2.60 (100.00) 18.40 2.60 (100.00) 46.00
  1. aHaplotypes estimated using all 17 SNPs.
  2. bHaplotypes estimated using SNPs from −1765 to +6249 (nine SNPs).
  3. cIn brackets, percentage of common haplotypes (frequency >5%).
  4. dIn brackets, percentage of the total common haplotypes (frequency >5%) detectable by using tag-SNPs.
  5. eOnly one tag-SNP has been used, since the second tag-SNP lies out of the analyzed region.