Table 5.
Comparative analysis of allele frequencies between the Kazakh population (present study) and other ethnic populations (HapMap data)
| Exact test of population differentiation (P value) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | ASW | CEU | CHB | CHD | GIH | JPT | LWK | MEX | MKK | TSI | YRI |
| rs3751812 | 0.26/0.11 (0.003) | 0.26/0.46 (<10−5) | 0.26/0.15 (0.01) | 0.26/0.15 (0.009) | 0.26/0.26 (1.000) | 0.26/0.18 (0.1) | 0.26/0.02 (<10−5) | 0.26/0.17 (0.06) | 0.26/0.13 (<10−5) | 0.26/0.46 (<10−5) | 0.26/0.07 (<10−5) |
| rs8050136 | 0.26/0.45 (<10−4) | 0.26/0.46 (<10−5) | 0.26/0.14 (0.002) | .26/0.16 (0.02) | 0.26/0.26 (1.000) | 0.26/0.18 (0.08) | 0.26/0.49 (<10−5) | 0.26/0.20 (0.09) | 0.26/0.48 (<10−5) | 0.26/0.46 (<10−5) | 0.26/0.46 (<10−5) |
| rs9939609 | 0.25/0.49 (<10−5) | 0.25/0.46 (<10−5) | 0.25/0.15 (0.01) | .25/0.16 (0.03) | 0.25/0.27 (0.8) | 0.25/0.19 (0.2) | 0.25/0.38 (<10−5) | NA | .25/0.47 (<10−5) | 0.25/0.47 (<10−5) | 0.25/0.49 (<10−5) |
| rs10811661 | 0.28/0.09 (<10−4) | 0.28/0.20 (0.02) | 0.28/0.42 (0.001) | 0.28/0.44 (<10−3) | 0.28/0.09 (<10−5) | 0.28/0.48 (<10−5) | 0.28/0.06 (<10−5) | 0.28/0.11 (<10−3) | 0.28/0.10 (<10−5) | 0.28/0.19 (0.01) | 0.28/0.02 (<10−5) |
| rs2383208 | 0.28/0.24 (0.5) | 0.28/0.21 (0.09) | .28/0.40 (0.004) | 0.28/0.41 (0.001) | 0.28/0.09 (<10−5) | 0.28/0.45 (<10−4) | 0.28/0.21 (0.2) | 0.28/0.14 (0.01) | .28/0.32 (0.2) | 0.28/0.19 (0.02) | 0.28/0.12 (<10−5) |
| rs1111875 | 0.41/0.23 (<10−5) | 0.41/0.42 (<10−5) | 0.41/0.32 (0.04) | 0.41/0.31 (0.06) | 0.41/0.41 (0.9) | 0.41/0.35 (0.09) | 0.41/0.19 (<10−5) | 0.41/0.26 (<10−5) | 0.41/0.24 (<10−5) | 0.41/0.40 (<10−5) | 0.41/0.13 (<10−5) |
| rs13266634 | 0.37/0.19 (<10−3) | 0.37/0.24 (<10−3) | 0 .37/0.47 (0.04) | 0.37/0.44 (0.2) | 0.37/0.23 (0.001) | .37/0.44 (0.2) | 0.37/0.06 (<10−5) | 0.37/0.19 (0.002) | 0.37/0.05(<10−5) | 0.37/0.25 (0.006) | 0.37/0.07(<10−5) |
| rs4506565 | 0.15/0.49 (<10−5) | 0.15/0.30 (<10−5) | 0.15/0.07 (0.01) | 0.15/0.04 (<10−3) | 0.15/0.30 (<10−5) | 0.15/0.03 (<10−4) | .15/0.49 (<10−5) | 0.15/0.28 (0.005) | 0.15/0.40 (<10−5) | 0.15/0.39 (<10−5) | 0.15/0.44 (<10−5) |
| rs5215 | 0 .34/0.19 (<10−5) | .34/0.40 (0.09) | 0.34/0.35 (0.7) | 0.34/0.35 (0.8) | 0.34/0.40 (0.2) | 0.34/0.34 (1.0) | 0.34/0.03 (<10−5) | 0.34/0.42 (0.3) | 0.34/0.06 (<10−5) | 0.34/0.29 (0.4) | 0.34/0.01 (<10−5) |
| rs7756992 | 0.33/0.46 (<10−5) | 0.33/0.28 (0.2) | 0.33/0.48 (<10−3) | 0.33/0.49 (<10−5) | 0.33/0.24 (0.07) | 0.33/0.46 (0.001) | 0.33/0.42 (<10−5) | 0.33/0.34 (0.9) | 0.33/0.41 (<10−5) | 0.33/0.24 (0.02) | 0.33/0.39 (<10−5) |
| rs4712523 | 0.32/0.40 (<10−5) | 0.32/0.24 (0.8) | 0.32/0.42 (0.02) | 0.32/0.41 (0.02) | 0.32/0.23 (0.04) | 0.32/0.41 (0.04) | 0.32/0.34 (<10−5) | 0.32/0.31 (0.6) | 0.32/0.46 (<10−5) | 0.32/0.28 (0.1) | 0.32/0.31 (<10−5) |
| rs9465871 | 0.30/0.46 (<10−5) | 0.30/0.16 (<10−5) | 0.30/0.50 (<10−5) | 0.30/0.48 (<10−5) | 0.30/0.22 (0.05) | 0.30/0.44 (<10−5) | 0.30/0.45 (<10−3) | 0.30/0.32 (0.8) | 0.30/0.46 (<10−5) | 0.30/0.16 (<10−4) | 0.30/0.39 (<10−5) |
| rs7961581 | 0.25/0.17 (0.2) | 0.25/0.25 (0.4) | 0.25/0.20 (0.06) | 0.25/0.19 (0.05) | 0.25/0.36 (0.003) | 0.25/0.23 (0.9) | 0.25/0.20 (0.3) | 0.25/0.15 (0.06) | 0.25/0.20 (0.3) | 0.25/0.40 (<10−3) | 0.25/0.17 (0.02) |
| rs864745 | 0.38/0.23 (0.01) | 0.38/0.49 (0.001) | 0.38/0.24 (0.002) | 0.38/0.22 (<10−3) | 0.38/0.22 (<10−3) | 0.38/0.21 (<10−5) | 0.38/0.20 (<10−5) | 0.38/0.38 (0.6) | 0.38/0.26 (<10−3) | 0.38/0.49 (0.006) | 0.38/0.23 (<10−4) |
| rs12779790 | NA | 0.17/0.23 (0.04) | 0.17/0.13 (0.8) | NA | NA | 0.17/0.12 (0.3) | NA | NA | NA | NA | 0.17/0.05 (0.001) |
| rs10490072 | 0.13/0.15 (0.6) | 0.13/0.27 (<10−5) | 0.13/0.02 (<10−4) | NA | 0.13/0.15 (0.3) | 0.13/0.01(<10−5) | 0.13/0.04(0.001) | 0.13/0.20(0.05) | 0.13/0.02(<10−5) | 0.13/0.21(0.009) | 0.13/0.04 (0.001) |
| rs10923931 | 0.06/0.35 (<10−5) | 0.06/0.09 (0.07) | 0.06/0.02 (0.3) | 0.06/0.02 (0.2) | 0.06/0.21 (<10−5) | 0.06/0.02 (0.2) | 0.06/0.46 (<10−5) | 0.06/0.09 (0.2) | 0.06/0.36 (<10−5) | 0.06/0.07 (0.2) | 0.06/0.38 (<10−5) |
| rs7578597 | 0.06/0.27 (<10−5) | 0.06/0.12 (<10−3) | 0.06/0.14 (<10−5) | 0.06/0.01 (0.008) | 0.06/0.17 (<10−5) | 0.06/0.01 (0.008) | 0.06/0.36 (<10−5) | 0.06/0.02 (0.3) | 0.06/0.19 (<10−5) | 0.06/0.06 (0.6) | 0.06/0.33 (<10−5) |
| rs2025804 | 0.36/0.17 (<10−5) | 0.36/0.38 (<10−5) | 0.36/0.16 (<10−5) | 0.36/0.11 (<10−5) | 0.36/0.21 (<10−5) | 0.36/0.15 (<10−5) | 0.36/0.22 (<10−5) | 0.36/0.35 (<10−5) | 0.36/0.15 (<10−5) | 0.36/0.27 (<10−5) | 0.36/0.23 (<10−5) |
| rs2641348 | 0.05/0.35 (<10−5) | 0.05/0.10 (0.01) | 0.05/0.02 (0.09) | 0.05/0.02 (0.08) | 0.05/0.22 (<10−5) | 0.05/0.02 (0.09) | 0.05/0.46 (<10−5) | 0.05/0.10 (0.06) | 0.05/0.36 (<10−5) | 0.05/0.08 (0.07) | 0.05/0.38 (<10−5) |
| rs9472138 | 0.19/0.13 (0.2) | 0.19/0.23 (0.2) | 0.19/0.13 (0.07) | NA | 0.19/0.22 (0.4) | 0.19/0.09 (0.001) | 0.19/0.23 (0.3) | 0.19/0.20 (0.4) | NA | 0.19/0.31 (<10−4) | 0.19/0.15 (0.1) |
| rs1042714 | NA | 0.28/0.47 (<10−5) | 0.28/0.12 (0.002) | NA | NA | 0.28/0.08 (<10−3) | NA | NA | NA | NA | 0.28/0.18 (0.03) |
| rs4994 | 0.17/0.08 (0.04) | 0.17/0.09 (0.003) | 0.17/0.11 (0.2) | 0.17/0.14 (0.2) | 0.17/0.11 (0.1) | 0.17/0.19 (0.06) | 0.17/ 0.09 (0.02) | 0.17/ 0.09 (0.03) | 0.17/0.13 (0.1) | 0.17/0.04 (<10−5) | 0.17/0.06 (<10−5) |
| rs1799883 | 0.35/0.22 (0.01) | 0.35/0.33 (0.2) | 0.35/0.32 (0.6) | 0.35/0.21 (0.001) | 0.35/0.36 (0.9) | 0.35/0.32 (0.6) | 0.35/0.19 (<10−5) | 0.35/0.30 (0.6) | 0.35/0.18 (<10−5) | 035/0.25 (0.04) | NA |
| rs1801282 | 0.14/0.02 (<10−3) | 0.14/0.10(0.2 | 0.14/0.05 (0.001) | 0.14/0.03 (<10−5) | 0.14/ 0.09 (0.09) | 0.14/0.03 (<10−4) | NA | 0.14/0.09 (0.5) | 0.14/0.02 (<10−5) | 0.14/0.07 (0.07) | 0.14/0 (<10−5) |
| rs8192678 | 0.39/0.07 (<10−5) | 0.39/0.35 (0.2) | 0.39/0.40 (0.6) | 0.39/0.40 (0.9) | 0.39/0.30 (0.05) | 0.39/0.47 (0.001) | 0.39/0.02 (<10−5) | 0.39/0.21 (<10−3) | 0.39/0.08 (<10−5) | 0.39/0.43 (0.5) | 0.39/0.04 (<10−5) |
| rs780094 | 0.35/0.12 (<10−5) | 0.35/0.41 (0.3) | 0.35/0.41 (<10−5) | NA | 0.35/0.20 (<10−4) | 0.35/0.42 (<10−5) | 0.35/0.10 (<10−5) | 0.35/0.34 (0.7) | NA | .35/0.50 (<10−4) | 0.35/0.12 (<10−5) |
| rs7944584 | 0.13/0.06 (<10−5) | 0.13/0.30 (<10−5) | 0.13/0.05 (<10−5) | NA | 0.13/0.22 (<10−5) | 0.13/0.02 (<10−5) | 0.13/0 (<10−5) | 0.13/0.19 (<10−5) | NA | 0.13/0.36 (<10−5) | 0.13/0 (<10−5) |
Notes ASW: African ancestry living in the southwest USA
CEU: Utah residents with Northern and Western European ancestry from the CEPH collection
CHB: Han Chinese population in Beijing, China
CHD: Chinese population in Metropolitan Denver, CO.
GIH: Gujarati Indian population in Houston, TX
JPT: Japanese population in Tokyo, Japan
LWK: Luhya population in Webuye, Kenya. MEX: Mexicans in Los Angeles, CA. МKK: Maasai in Kinayawa, Kenya
NA: Not availables
TSI: Tuscan population in Italy
YRI: Yoruban population in Ibadan, Nigeria
NA: data not available from the HapMap
The values represent the minor allele frequencies in Kazakh population/ in the other ethnicities (p value)