Table 1. Selection of SNPs across RB1.
SNP ID | Genomic location | Nucleotide changea | SNPs chosen initially for genotyping | SNP reported by NIEHS with MAF>0.05 | Tag SNP | Tagging SNP(s) | r p 2 |
---|---|---|---|---|---|---|---|
rs1573601 | Upstream | c>a | ✓ | rs1981434, rs4151540, rs3092904 (g/+/a haplotype) | 0.93 | ||
rs1981434 | Intron 1 | c>g | ✓ | ✓ | rs1981434 | 1.0 | |
rs2854345 | Intron 2 | a>g | ✓ | ✓ | ✓ | rs2854345 | 1.0 |
rs4151437 | Intron 2 | g>a | ✓ | rs4151551 | 0.80 | ||
rs4151438 | Intron 2 | c>g | ✓ | FAILb | rs2854345 | 0.19 | |
rs520342 | Intron 3 | c>t | ✓ | ✓ | ✓ | rs520342 | 1.0 |
rs4151450 | Intron 3 | g>c | ✓ | rs399413 | 0.85 | ||
rs198619 | Intron 7 | t>a | ✓ | rs399413 | 0.84 | ||
rs4151510 | Intron 11 | g>a | ✓ | rs4151620 | 1.0 | ||
rs4151520 | Intron 11 | g>a | ✓ | rs520342 | 0.96 | ||
rs399413 | Intron 12 | g>a | ✓ | ✓ | ✓ | rs399413 | 1.0 |
rs4151540 | Intron 17 | ->aa | ✓ | ✓ | rs4151540 | 1.0 | |
rs198610 | Intron 17 | g>t | ✓ | ?c | ? | ||
rs4151551 | Intron 17 | g>t | ✓ | ✓ | rs4151551 | 1.0 | |
rs2227311 | Intron 17 | t>c | ✓ | ✓ | ✓ | rs4151620 | 1.0 |
rs2854344 | Intron 17 | g>a | ✓ | ?c | ? | ||
rs9535032 | Intron 17 | a>g | ✓ | ?c | ? | ||
rs425834 | Intron 17 | a>g | ✓ | ✓ | rs425834 | 1.0 | |
rs1951775 | Intron 17 | g>t | ✓ | rs399413 | 0.85 | ||
rs198570 | Intron 17 | g>t | ✓ | rs3092904 | 1.0 | ||
rs4151580 | Intron 18 | g>a | ✓ | Not polymd | rs4151580 | 1.0 | |
rs4151584 | Intron 18 | t>c | ✓ | FAILb | rs2854345 | 0.28 | |
rs198580 | Intron 19 | a>g | ✓ | ?c | ? | ||
rs198590 | Intron 21 | g>a | ✓ | rs520342 | 1.0 | ||
rs4151611 | Intron 24 | g>a | ✓ | ✓ | rs4151611 | 1.0 | |
rs4151618 | Intron 24 | t>c | ✓ | rs4151611 | 1.0 | ||
rs4151620 | Intron 24 | c>g | ✓ | ✓ | ✓ | rs4151620 | 1.0 |
rs3092904 | Intron 24 | t>a | ✓ | ✓ | ✓ | rs3520342 | 0.98 |
rs4151636 | Downstream | c>g | ✓ | ✓ | rs4151636 | 1.0 |
The most common allele is given first.
The SNP was initially selected for genotyping but the assay could not be designed.
The contribution of the SNP to the tagging of other identified SNP could not be estimated.
The SNP was not polymorphic in the British population.