TABLE 1.
Characteristics of the 16 highly divergent loci identified in our screen with ABO and HLA for comparison
| Minor allele freq (no. of haplotypes sampled)b
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Locus | Chromosome, band | build35.1 position | MAXDIVa | Chinese American | Caucasian American | African American | FST | Human–chimp divergence (%) | No. of conserved bpd (P-value)e | Annotation |
| bs001 | 1q42.13 | chr1:225,180,594–225,185,593 | 17 | NA | NA | NA | NA | 0.92 | 12 (0.68) | Adjacent to 774-bp terminal coding exon of RHOU, which contains no known polymorphisms. |
| bs002 | 1q43 | chr1:234,960,748–234,965,747 | 41 | 0.820 (50) | 0.688 (64) | 0.469 (64) | 0.20 | 1.50 | 23 (0.62) | 500 kbp from nearest annotated gene. |
| bs003 | 3p25.3 | chr3:11,615,674–11,620,673 | 39 | NA | NA | NA | NA | 2.00 | 214 (0.22) | Contains a 172-bp internal coding exon of VGLL4, which has no high-minor- allele-frequency polymorphisms. |
| bs004 | 5q33.2 | chr5:152,911,118–152,916,117 | 38 | 0.078 (64) | 0.516 (64) | 0.145 (62) | 0.47 | 1.18 | 39 (0.51) | In the middle of 150-kbp intron of GRIA1. |
| bs005 | 3q26.31 | chr3:176,595,380–176,600,379 | 19 | NA | NA | NA | NA | 1.09 | 158 (0.29) | In the middle of 130-kbp intron of NAALADL2. |
| bs006 | 4q31.22 | chr4:147,247,730–147,252,729 | 22 | NA | NA | NA | NA | 0.93 | 27 (0.51) | 20 kbp downstream of LOC152485. |
| bs007 | 4q35.2 | chr4:189,958,640–189,963,639 | 49 | 0.417 (60) | 0.766 (64) | 0.476 (62) | 0.15 | 1.19 | 8 (0.63) | In exon of GENSCAN- predicted gene with no mRNA support and no homology between predicted amino acid sequence and known proteins. |
| bs008 | 7p21.3 | chr7:8,407,241–8,412,240 | 31 | 0.233 (60) | 0.048 (62) | 0.328 (64) | 0.60 | 1.50 | 205 (0.21) | 200 kbp away from nearest annotated gene. |
| bs009c | 7q21.13 | chr7:88,955,055–88,960,054 | 63 | 0.621 (58) | 0.741 (58) | 0.414 (58) | 0.23 | 1.63 | 0 (1) | In the middle of 300-kbp intron of NXPH1. |
| bs010 | 7q34 | chr7:141,399,700–141,404,699 | 37 | 0.617 (60) | 0.583 (60) | 0.435 (62) | 0.24 | 1.30 | 129 (0.31) | 5 kbp downstream of TRY1, which has no coding known polymorphisms. |
| bs011 | 7q35 | chr7:146,451,078–146,456,077 | 33 | NA | NA | NA | NA | 1.51 | 19 (0.60) | In the middle of 100-kbp intron of CNTNAP2. |
| bs012 | 8p23.2 | chr8:3,887,626–3,892,625 | 45 | NA | NA | NA | NA | 4.70 | 0 (1) | 10 kbp downstream of CSMD1 exon, which has no known polymorphisms. |
| bs013 | 8q11.21 | chr8:50,278,353–50,283,352 | 47 | 0.391 (64) | 0.468 (62) | 0.177 (62) | 0.42 | 1.22 | 0 (1) | 120 kbp downstream of nearest predicted gene with mRNA support. |
| bs014 | 8q12.1 | chr8:57,926,636–57,931,635 | 47 | 0.567 (60) | 0.406 (64) | 0.133 (60) | 0.43 | 1.68 | 73 (0.39) | 100 kbp upstream of nearest predicted gene with mRNA support. |
| bs015 | 8q22.1 | chr8:96,581,055–96,586,054 | 25 | NA | NA | NA | NA | 1.12 | 440 (0.06) | 300 kbp away from nearest annotated gene. |
| bs016 | 8q24.23 | chr8:138,682,749–138,687,748 | 48 | 0.170 (62) | 0.161 (62) | 0.452 (62) | 0.47 | 1.42 | 425 (0.06) | 100 kbp upstream of nearest predicted exon with mRNA support. |
| ABO | 9q34.2 | chr9:133,160,949–133,165,948 | 49 | NA | NA | NA | NA | 1.06 | 138 (0.33) | Contains last four exons of ABO. |
| HLA | 6p21.32 | chr6:32,686,220–32,691,219 | 409 | NA | NA | NA | NA | 0.96 | 0 (1) | Midway between DRB1 and DQA1, which are separated by 50 kbp. |
a
Number of nucleotide differences in this 5-kbp window between the most dissimilar haplotypes tested.
b
Allele defined by a single “tag” SNP, chosen as described in the text; the “minor allele” is the allele that is less frequent in the African-American population.
c
Resequenced original site, but probe for identifying appropriate fosmids was in 3-kbp upstream region.
d
Posterior probability of conservation >0.9 according to Siepel et al. (2005).
e
Probability that a randomly chosen 5-kbp window from the same chromosome would contain at least that number of conserved base pairs in that window.