Table 2.
Single nucleotide polymorphisms detected in the study population
| Reference SNP identifier | Chromosome position | SNP frequency by sex, proportion deficient (n/N) | Total SNP frequency, proportion deficient (n/N) | Ancestral: alternate allele | Function | |||
|---|---|---|---|---|---|---|---|---|
| Male hemizygotes | Female homozygotes | Female heterozygotes | Hemizygous/homozygous | Heterozygous | ||||
| rs28470352 | 153,753,490 | 8.3 (10/121) | 5.8 (5/87) | 20.7 (18/87) | 5.8 (12/208) | 10.1 (21/208) | T:A | Intergenic variant |
| rs61042368 | 153,755,336 | 5.0 (6/120) | 1.2 (1/86) | 1.2 (1/86) | 2.4 (5/206) | 1.5 (3/206) | G:A | Downstream gene variant |
| rs12389569 | 153,757,734 | 0 (0/120) | 0 (0/85)* | 2.4 (2/85) | 0 (0/205) | 1.0 (2/205) | G:A | Downstream gene variant |
| b36_153413623 | 153,760,429 | 1.7 (2/121) | 2.4 (2/85) | 3.5 (3/85) | 1.9 (4/206) | 1.5 (3/206) | G:A | Synonymous variant |
| rs2230036 | 153,760,953 | 5.9 (7/119) | 1.2 (1/86) | 1.2 (1/86) | 2.4 (5/205) | 2.0 (4/205) | C:T | Synonymous variant |
| rs73573478 | 153,761,564 | 8.9 (11/123) | 2.2 (2/90) | 4.4 (4/90) | 4.7 (10/213) | 3.3 (7/213) | G:A | Non coding exon variant |
| rs5986990 | 153,761,628 | 7.8 (9/115) | 5.9 (5/85) | 21.2 (18/85) | 6.0 (12/200) | 10.0 (20/200) | G:A | Non coding exon variant |
| rs2515905 | 153,762,075 | 3.3 (4/120) | 1.2 (1/87) | 4.6 (4/87) | 2.4 (5/207) | 1.9 (4/207) | G:A | Intron variant |
| rs2515904 | 153,762,771 | 3.3 (4/121) | 1.2 (1/87) | 4.6 (4/87) | 2.4 (5/208) | 1.9 (4/208) | G:C | Intron variant |
| rs1050829 | 153,763,492 | 8.3 (10/121) | 7.9 (7/89) | 20.2 (18/89) | 6.7 (14/210) | 10.0 (21/210) | A:G | Missense variant |
| rs1050828 | 153,764,217 | 3.3 (4/120) | 0 (0/90) | 3.3 (3/90) | 1.9 (4/210) | 1.4 (3/210) | G:A | Missense variant |
| rs762515 | 153,764,528 | 7.7 (9/117) | 5.8 (5/86) | 20.0 (17/86) | 5.9 (12/203) | 9.4 (19/203) | T:C | Intron variant |
| rs762516 | 153,764,663 | 3.3 (4/121) | 1.2 (1/87) | 4.6 (4/87) | 2.4 (5/208) | 1.9 (4/208) | C:T | Intron variant |
| rs113492957 | 153,773,062 | 9.2 (11/120) | 2.3 (2/86) | 3.5 (3/86) | 4.9 (10/206) | 2.9 (6/206) | C:T | Intron variant |
| rs111827785 | 153,775,785 | 18.2 (22/121) | 9.6 (8/83) | 24.1 (20/83) | 12.8 (26/204) | 11.8 (24/204) | T:C | 5′ UTR |
| rs60030796 | 153,836,171 | 5.0 (6/119) | 4.6 (4/87) | 12.6 (11/87) | 3.4 (7/206) | 6.8 (14/206) | A:G | Downstream gene variant |
SNP single nucleotide polymorphism
The following SNPs were monomorphic and excluded from further analysis: rs5030869, rs76723693 (968), rs137852328 (680), rs5030868, rs5030872 (542), and rs137852318. *SNP with minor allele frequency < 1% and was omitted from further analysis. Italicized are the well-known rs1050828 (G202A) and rs1050828 (A376G) African polymorphisms. Bolded and italicized (rs2515904) indicates a SNP that was detected in individuals who carried the 376 and 202 variants