Table 4. Linkage disequilibrium between the -35 SNP and the HLA-C alleles present in the Black and Caucasian South African population groups.
| Black Individuals (n1 = 168) | Caucasian Individuals (n1 = 97) | |||||||
| HLA-C Allele | -35 SNP Allele | Frequency2 | D’3 | p-value4 | -35 SNP Allele | Frequency2 | D’3 | p-value4 |
| 01∶02 | – | – | – | – | C | 0.0155 (35) | 0.65 | <0.05 |
| 02∶02 | C | 0.0149 (5) | 1.00 | <0.05 | C | 0.0723 (14) | 1.00 | <0.01 |
| 02∶05 | T | 0.0030 (1) | 1.00 | NS | C | 0.0052 (1) | 1.00 | NS |
| 02∶10 | T | 0.0655 (22) | 0.59 | <0.05 | – | – | – | – |
| 03∶02 | C | 0.0149 (5) | 1.00 | <0.01 | – | – | – | – |
| 03∶03 | C | 0.0030 (1) | 1.00 | NS | T | 0.0619 (12) | 1.00 | <0.05 |
| 03∶04 | T | 0.0446 (15) | 1.00 | <0.01 | T | 0.0567 (11) | 1.00 | <0.05 |
| 03∶16 | – | – | – | – | T | 0.0052 (1) | 1.00 | NS |
| 04∶01 | T | 0.1250 (42) | 1.00 | <0.01 | T | 0.0876 (17) | 1.00 | <0.01 |
| 04∶04 | T | 0.0030 (1) | 1.00 | NS | – | – | – | – |
| 04∶08 | – | – | – | – | T | 0.0052 (1) | 1.00 | NS |
| 05∶01 | C | 0.0060 (2) | 0.49 | NS | T | 0.0412 (8) | 0.28 | NS |
| 06∶02 | C | 0.1488 (50) | 1.00 | <0.01 | C | 0.0773 (15) | 1.00 | <0.01 |
| 06∶06 | C | 0.0030 (1) | 1.00 | NS | – | – | – | – |
| 06∶11 | C | 0.0030 (1) | 1.00 | NS | C | 0.0052 (1) | 1.00 | NS |
| 07∶01 | T | 0.0506 (17) | 0.16 | NS | T | 0.1753 (34) | 1.00 | <0.01 |
| 07∶02 | T | 0.0595 (20) | 0.86 | <0.01 | T | 0.1443 (28) | 1.00 | <0.01 |
| 07∶04 | T | 0.0149 (5) | 1.00 | NS | T | 0.0103 (2) | 1.00 | NS |
| 07∶06 | C | 0.0387 (13) | 1.00 | <0.01 | C | 0.0206 (4) | 1.00 | <0.01 |
| 07∶11 | T | 0.0030 (1) | 1.00 | NS | – | – | – | – |
| 07∶18 | C | 0.0417 (14) | 0.89 | <0.01 | C | 0.0155 (3) | 1.00 | <0.01 |
| 08∶01 | T | 0.0030 (1) | 1.00 | NS | T | 0.0052 (1) | 1.00 | NS |
| 08∶02 | T | 0.0119 (4) | 0.42 | NS | C | 0.0103 (2) | 0.31 | NS |
| 08∶04 | C | 0.0149 (5) | 0.24 | NS | C | 0.0103 (2) | 1.00 | <0.05 |
| 12∶02 | – | – | – | – | C | 0.0103 (2) | 1.00 | <0.05 |
| 12∶03 | C | 0.0149 (5) | 1.00 | <0.01 | C | 0.0206 (4) | 1.00 | <0.01 |
| 14∶02 | C | 0.0060 (2) | 1.00 | <0.05 | C | 0.0103 (2) | 1.00 | <0.05 |
| 15∶02 | T | 0.0060 (2) | 1.00 | NS | T | 0.0258 (5) | 1.00 | NS |
| 15∶05 | T | 0.0089 (3) | 1.00 | NS | – | – | – | – |
| 15:xx | T | 0.0060 (2) | 1.00 | NS | – | – | – | – |
| 16∶01 | T | 0.0655 (22) | 0.76 | <0.01 | T | 0.0670 (13) | 1.00 | <0.05 |
| 16∶02 | – | – | – | – | T | 0.0103 (2) | 1.00 | NS |
| 17∶01 | T | 0.1131 (38) | 1.00 | <0.01 | T | 0.0052 (1) | 1.00 | NS |
| 18∶01 | T | 0.0149 (5) | 1.00 | NS | – | – | – | – |
| 18∶02 | T | 0.0298 (10) | 1.00 | <0.05 | – | – | – | – |
1
the total number of individuals genotyped in each population group.
2
the observed frequency of each two-locus haplotype.
3
Lewontin's D' measure of linkage disequilibrium [19].
4
p-values are calculated using an exact test for linkage disequilibrium [20], and are significant at p<0.05.
5
the number of chromosomes on which the two-locus haplotype was found to occur.