Extended Data Table 2. Frequency of common C4 alleles and their LD-based correlation with HLA alleles in European ancestry and African American cohorts.
For each common C4 allele and HLA gene, the allele with strongest LD (r2) is listed if present on more than half of the haplotypes with that C4 allele (exact fraction in %). r2 values greater than 0.4 are highlighted to point out particularly strong C4-HLA allele correlations, such as for several HLA alleles with the C4-B(S) allele in European ancestry individuals. Some common C4 alleles are further subdivided into distinct haplotypes used in imputation (and in Fig. 1b), as defined by shared alleles from variants flanking C4. Note that some alleles such as C4-A(L)-A(L)-3 are present at a low frequency in African Americans that might reflect their presence on admixed European-origin haplotypes spanning this region, whereas others such as C4-B(S) are likely to also exist on African haplotypes – these differences between C4 alleles are also reflected in the similarity of LD with HLA alleles to the corresponding row of the European ancestry section.
| European ancestry | |||||||||||||||||||
|
A |
B |
C |
C4 allele | Allele Frequency |
DRB1 |
DQA1 |
DQB1 |
||||||||||||
| allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | ||
| 01:01 | 69 | 0.27 | 08:01 | 93 | 0.75 | 07:01 | 93 | 0.57 | B(S) | 13.7% | 03:01 | 94 | 0.71 | 05:01 | 94 | 0.7 | 02:01 | 94 | 0.7 |
| A(L) | 4.8% | ||||||||||||||||||
| 06:02 | 69 | 0.31 | A(L)-B(S)-1 | 6.1% | 07:01 | 74 | 0.25 | 02:01 | 74 | 0.25 | |||||||||
| 44:03 | 54 | 0.28 | 16:01 | 53 | 0.39 | A(L)-B(S)-2 | 4.5% | 07:01 | 57 | 0.1 | 02:01 | 57 | 0.1 | 02:02 | 55 | 0.14 | |||
| A(L)-B(S)-3 | 3.8% | ||||||||||||||||||
| A(L)-B(S)-4 | 4.5% | ||||||||||||||||||
| 07:02 | 64 | 0.42 | 07:02 | 63 | 0.35 | A(L)-B(L)-1 | 15.5% | 15:01 | 73 | 0.49 | 01:02 | 74 | 0.32 | 06:02 | 70 | 0.47 | |||
| A(L)-B(L)-2 | 23.1% | ||||||||||||||||||
| 35:01 | 55 | 0.2 | 04:01 | 57 | 0.09 | A(L)-A(L)-1 | 3.2% | 01:01 | 65 | 0.14 | 01:01 | 65 | 0.11 | 05:01 | 64 | 0.1 | |||
| A(L)-A(L)-2 | 2.1% | 13:01 | 67 | 0.16 | 01:03 | 65 | 0.13 | 06:03 | 67 | 0.15 | |||||||||
| 02:01 | 65 | 0.03 | 44:02 | 74 | 0.24 | 05:01 | 72 | 0.23 | A(L)-A(L)-3 | 4.5% | 04:01 | 80 | 0.29 | 03:03 | 79 | 0.37 | 03:01 | 82 | 0.15 |
| African American | |||||||||||||||||||
|
A |
B |
C |
C4 allele | Allele Frequency |
DRB1 |
DQA1 |
DQB1 |
||||||||||||
| allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | allele | % | r2 | ||
| B(S) | 5.0% | 01:02 | 51 | 0.01 | |||||||||||||||
| A(L) | 7.5% | ||||||||||||||||||
| A(L)-B(S)-1 | 14.1% | ||||||||||||||||||
| A(L)-B(S)-2 | 18.1% | ||||||||||||||||||
| A(L)-B(S)-3 | 17.7% | ||||||||||||||||||
| A(L)-B(S)-4 | 6.5% | ||||||||||||||||||
| A(L)-B(L)-1 | 4.4% | 15:01 | 67 | 0.2 | 01:02 | 72 | 0.04 | 06:02 | 59 | 0.06 | |||||||||
| A(L)-B(L)-2 | 4.5% | ||||||||||||||||||
| A(L)-A(L)-1 | 0.7% | 01:01 | 57 | 0.07 | 01:01 | 53 | 0.01 | ||||||||||||
| A(L)-A(L)-2 | 0.8% | ||||||||||||||||||
| 02:01 | 72 | 0.03 | 44:02 | 86 | 0.31 | 05:01 | 78 | 0.17 | A(L)-A(L)-3 | 0.8% | 04:01 | 93 | 0.27 | 03:03 | 86 | 0.14 | 03:01 | 87 | 0.03 |