TABLE 2.
Estimated haplotype frequencies in three ethnic populations for the central 16 SNPs in theLPL gene
| Japanese
|
African Americans
|
Caucasians
|
|||||
|---|---|---|---|---|---|---|---|
| Haplotype class inferred from all 16 SNPsa | Haplotype (from SNP9 to SNP24) |
Frequency (%) |
(Order)b | Frequency (%) |
(Order)b | Frequency (%) |
(Order)b |
| HAP1 | TTGCATCCGAACCTCT | 63.9 | (1) | 31.5 | (1) | 42.5 | (1) |
| HAP2 | TTGCATCCGAACCTCG | 20.2 | (2) | 6.4 | (6) | 26.5 | (2) |
| HAP3 | CCCAGGCCAGTTCCAT | 5.3 | (4) | 10.5 | (2) | 11.0 | (3) |
| HAP4 | CCGCGGGTGATCACCT | 6.9 | (3) | 6.5 | (5) | 9.9 | (4) |
| HAP5 | TTGCGTCCGATCCCCT | — | — | 8.5 | (4) | 2.0 | (6) |
| HAP6 | CCCAGGCCGATCCCCT | — | — | 9.3 | (3) | — | — |
| HAP7 | TTGCGGCCGGTCCCCT | — | — | 5.9 | (7) | — | — |
| HAP8 | TTGCGGCCAGTTCCAT | — | — | — | — | 5.0 | (5) |
| HAP9 | TTGCGGCCGGTCCCAT | — | — | 3.4 | (8) | — | — |
| HAP10 | TTGCGTCCGAACCTCT | — | — | 3.0 | (9) | — | — |
| HAP11 | CCCCGGCCGATCCCCT | — | — | 2.1 | (10) | — | — |
| HAP12 | TTGCATCCGGACCTCT | — | — | 2.0 | (11) | — | — |
| HAP13 | CCCAGGCCAGTCCCAT | — | — | 2.0 | (12) | — | — |
| HAP14 | CCCAGGCCGGTCCCAT | — | — | 2.0 | (13) | — | — |
| Haplotype class inferred from 6 SNPs in SNP cluster A (SNP9, SNP10, SNP13, SNP14, SNP19 and SNP22)c | |||||||
| A-1 (HAP1 + 2 + 12) | TT--AT----A--T-- | 84.5 | (1) | 39.9 | (1) | 69.0 | (1) |
| A-2 (HAP3 + 4 + 6 + 11 + 13 + 14) |
CC--GG----T--C-- | 14.6 | (2) | 34.0 | (2) | 21.5 | (2) |
| A-3 (HAP7 + 8 + 9) | TT--GG----T--C-- | — | — | 9.6 | (3) | 5.0 | (3) |
| A-4 (HAP5) | TT--GT----T--C-- | — | — | 8.7 | (4) | — | — |
| Haplotype class inferred from 4 SNPs in SNP cluster B (SNP17, SNP18, SNP20 and SNP23)c | |||||||
| B-1 (HAP1 + 2 + 4 + 5 + 6 + 10 + 11) |
--------GA-C--C- | 93.4 | (1) | 69.3 | (1) | 84.0 | (1) |
| B-2 (HAP3 + 8) | --------AG-T--A- | 5.8 | (2) | 12.0 | (2) | 16.0 | (2) |
| B-3 (HAP7 + 12) | --------GG-C--C- | — | — | 8.7 | (3) | — | — |
| B-4 (HAP9 + 14) | --------GG-C--A- | — | — | 6.4 | (4) | — | — |
| Haplotype class inferred from 3 SNPs in SNP cluster C (SNP15, SNP16 and SNP21)c | |||||||
| C-1 (HAP1 + 2 + 3 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14) |
------CC----C--- | 90.7 | (1) | 92.0 | (1) | 89.5 | (1) |
| C-2 (HAP4) | ------GT----A--- | 9.3 | (2) | 6.9 | (2) | 9.9 | (2) |
a
Among 25 SNPs genotyped in the LPL gene (Table 1, Figure 2C), the central 16 SNPs (SNP9–SNP24 spanning 8.5 kbp) were used for the estimation of haplotype classes because they formed a haplotype block. While a number of haplotype classes were inferred from these SNPs, 14 had a frequency of at least 2% in the Japanese, African American, or Caucasian population, and they were numbered by the frequency order calculated from the three ethnic populations combined.
b
The frequency order shown in the parentheses was determined by calculating the percentage of the corresponding haplotype class in each ethnic group.
c
SNP clusters are defined in Figure 2B.