Table 2.
Computational haplotype determination using PHASE.
| Star allele | Allele carries | Haplotype frequency dataset_all n=6,324 | Haplotype frequency dataset_E n=2,964 | Haplotype frequency dataset_A n=1,218 | Haplotype frequency dataset_E n=2,964 | Haplotype frequency dataset_A n=1,218 |
|---|---|---|---|---|---|---|
| All samples phased together; n=number of alleles | Phased E only | Phased A only | ||||
| n= Number of allele (% of given allele) | ||||||
| *1 | none | 2,236 (94.6%) | 1,104 (98.6%) | 304 (76.9%) | 1,110 (99.1%) | 280 (70.7%) |
| rs5758550 (enhancer SNP) | 121 (5.1%) | 12 (1%) | 91 (23%) | 6 (0.5%) | 116 (29.2%) | |
| rs1080985 (−1584C>G)+ rs5758550 (enhancer SNP) | 3 (0.1%) | 2 (0.1%) | 0 (0%) | 3 (0.2%) | 0 (0%) | |
| rs1080985 (−1584C>G) | 2 (0%) | 1 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | |
| *10 | none | 248 (98.8%) | 48 (97.9%) | 43 (97.7%) | 48 (97.9%) | 42 (95.4%) |
| rs5758550 (enhancer SNP) | 3 (1.1%) | 1 (2%) | 1 (2.2%) | 1 (2%) | 1 (2.2%) | |
| rs5030655 (*6) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2.2%) | |
| *17 | none | 4 (1.6%) | 0 (0%) | 3 (1.5%) | 0 (0%) | 5 (2.5%) |
| rs5758550 (enhancer SNP) | 236 (98.3%) | 13 (100%) | 194 (98.4%) | 13 (100%) | 192 (97.4%) | |
| *2 | none | 66 (6%) | 3 (0.5%) | 60 (27.6%) | 4 (0.7%) | 63 (28.6%) |
| rs1080985 (−1584C>G) | 33 (3%) | 18 (3.5%) | 2 (0.9%) | 17 (3.3%) | 0 (0%) | |
| rs5758550 (enhancer SNP) | 94 (8.6%) | 11 (2.1%) | 65 (29.9%) | 11 (2.1%) | 65 (29.5%) | |
| rs1080985 (−1584C>G)+ rs5758550 (enhancer SNP) | 898 (82.3%) | 476 (93.7%) | 90 (41.4%) | 477 (93.7%) | 92 (41.8%) | |
| *29 | none | 113 (87.5%) | 3 (100%) | 94 (87%) | 2 (100%) | 106 (99%) |
| rs5758550 (enhancer SNP) | 15 (11.6%) | 0 (0%) | 14 (12.9%) | 0 (0%) | 1 (0.9%) | |
| rs1080985 (−1584C>G)+ rs5758550 (enhancer SNP) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | |
| *3 | none | 66 (100%) | 48 (100%) | 4 (100%) | 48 (100%) | 4 (100%) |
| *35 | rs1080985 (−1584C>G) | 7 (2.9%) | 7 (4.3%) | 0 (0%) | 9 (5.5%) | 0 (0%) |
| rs1080985 (−1584C>G)+ rs5758550 (enhancer SNP) | 229 (97%) | 154 (95.6%) | 4 (100%) | 152 (94.4%) | 4 (100%) | |
| *4 | none | 974 (99.2%) | 561 (99.1%) | 95 (100%) | 561 (99.1%) | 95 (100%) |
| rs5758550 (enhancer SNP) | 1 (0.1%) | 1 (0.1%) | 0 (0%) | 1 (0.1%) | 0 (0%) | |
| *4.012 | none | 6 (0.6%) | 4 (0.7%) | 0 (0%) | 4 (0.7%) | 0 (0%) |
| *40 | none | 12 (100%) | 0 (0%) | 10 (100%) | 0 (0%) | 10 (100%) |
| *41 | none | 489 (97.9%) | 282 (97.9%) | 32 (94.1%) | 276 (95.8%) | 30 (96.7%) |
| rs5758550 (enhancer SNP) | 9 (1.8%) | 5 (1.7%) | 2 (5.8%) | 11 (3.8%) | 1 (3.2%) | |
| rs1080985 (−1584C>G)+ rs5758550 (enhancer SNP) | 1 (0.2%) | 1 (0.3%) | 0 (0%) | 1 (0.3%) | 0 (0%) | |
| *45 | none | 56 (98.2%) | 1 (100%) | 41 (97.6%) | 1 (100%) | 41 (97.6%) |
| rs5758550 (enhancer SNP) | 1 (1.7%) | 0 (0%) | 1 (2.3%) | 0 (0%) | 1 (2.3%) | |
| *5 | none | 199 (85%) | 88 (90.7%) | 45 (72.5%) | 88 (90.7%) | 56 (90.3%) |
| rs5758550 (enhancer SNP) | 35 (14.9%) | 9 (9.2%) | 17 (27.4%) | 9 (9.2%) | 6 (9.6%) | |
| *6 | none | 39 (100%) | 32 (100%) | 1 (100%) | 32 (100%) | 1 (100%) |
| *69 | none | 1 (100%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| *9 | none | 126 (100%) | 79 (100%) | 5 (100%) | 79 (100%) | 5 (100%) |
Phasing was performed using dataset_all (all samples, n=3,162) and frequencies for samples with European and African ancestry calculated after phasing was performed. Phasing for dataset_E (samples with European ancestry, n=1,482) and dataset_A (samples with African ancestry, n=609) was performed on each dataset separately. Frequency denotes the frequency of the haplotype per PHASE output. The left-hand column provides the core star allele designation to which a haplotype matches. *4.012 denotes a *4 suballele lacking 100C>T, a SNP that is present in all other defined *4 suballeles. Of note, dbSNP reports rs1080985 as G>C (gnomAD MAF=0.2) while we refer to “C” as reference and “G” as variant. none denotes that allele does not have rs5758550 ("enhancer" SNP) or rs1080985 (-1584C>G).