Table 2.
Frequencies of identified CXCR6 single nucleotide polymorphisms (SNPs) within the Black (n=41) and Caucasian (n=40) study populations as determined through full length sequencing of CXCR6
| Location on gene | SNP Position | Base change (wt/mut) | Accession numbera | n (Minor allele frequency)b | |
|---|---|---|---|---|---|
| Blacksc | Caucasiansc | ||||
| 5' flanking region (1 689 bp) | −4498 | T/A | rs55920693 | 0 | 7 (0.088) |
| −4495 | G/A | rs3774640 | 12 (0.146) | 16 (0.200) | |
| −4377 | C/G | NI-1 | 1 (0.012) | 0 | |
| −4320 | G/A | rs3774639 | 5 (0.061) | 34 (0.425) | |
| −4087 | C/T | rs3774638 | 12 (0.146) | 16 (0.200) | |
| −4077 | G/A | rs115192433 | 4 (0.049) | 0 | |
| −3996 | G/A | rs56354570 | 0 | 1 (0.013) | |
| −3877 | C/T | rs7627147 | 26 (0.317) | 1 (0.013) | |
| −3674 | G/C | rs2234350 | 6 (0.073) | 20 (0.250) | |
| −3651 | G/A | rs2234351 | 12 (0.146) | 16 (0.200) | |
| −3466 | A/G | rs2234352 | 7 (0.085) | 0 | |
| −3173 | T/C | rs5375415933 | 0 | 1 (0.013) | |
|
| |||||
| Intron (2 921bp) | −2851 | T/C | rs55642383 | 1 (0.012) | 0 |
| −2627 | C/G | rs6785091 | 40 (0.488) | 8 (0.100) | |
| −2376 | T/C | rs6802841 | 4 (0.049) | 0 | |
| −1922 | T/C | rs56196539 | 5 (0.061) | 0 | |
| −1755 | A/C | rs3774635 | 21 (0.256) | 34 (0.425) | |
| −1695 | G/A | rs56184849 | 1 (0.012) | 0 | |
| −1629 | A/G | NI-2 | 1 (0.012) | 0 | |
| −1532 | G/C | rs3774634 | 22 (0.268) | 34 (0.425) | |
| −1351 | C/A | rs936939 | 12 (0.146) | 16 (0.200) | |
| −1091 | C/T | rs146431762 | 3 (0.037) | 0 | |
| −975 | G/A | rs6766548 | 3 (0.037) | 1 (0.013) | |
| −678 | G/A | rs74427539 | 2 (0.024) | 0 | |
| −108 | G/C | rs2234353 | 1 (0.012) | 0 | |
|
| |||||
| ORF (1 029 bp) | +7 | G/A | rs2234355 | 42 (0.512) | 1 (0.013) |
|
| |||||
| 3' UTR (2 369 bp) | +1071 | G/T | rs2234358 | 45 (0.549) | 41 (0.500) |
| +1150 | T/C | rs2234359 | 15 (0.183) | 0 | |
| +1546 | T/C | rs17078463 | 3 (0.037) | 1 (0.013) | |
| +1603 | G/A | rs60514862 | 1 (0.012) | 0 | |
| +1605 | C/G | rs55698153 | 3 (0.037) | 0 | |
| +1622 | A/G | NI-3 | 0 | 1 (0.013) | |
| +1900 | C/T | rs56332428 | 4 (0.049) | 7 (0.088) | |
| +1923 | C/T | rs9825221 | 8 (0.098) | 0 | |
| +1948 | G/T | rs71325095 | 2 (0.024) | 7 (0.088) | |
| +2016 | T/C | rs114052321 | 10 (0.122) | 0 | |
| +2144 | A/G | rs17078464 | 25 (0.305) | 1 (0.013) | |
| +2244 | A/G | rs2054866 | 21 (0.256) | 34 (0.425) | |
a
Accession numbers of SNPs detected in this study which been previously reported in the SNP database (dbSNP) are listed here, NI indicates putative newly identified polymorphisms not found in dbSNP.
b
Frequency was calculated for both populations using total number of alleles, i.e., n=82 for Black individuals and n=80 for Caucasian individuals.
c
Grey shading highlights poylmorphisms where frequencies differ significantly (P<0.05) between the two study populations.