Table 1—

Tagging(tag) single nucleotide polymorphism (SNP) selection using the LDSelect program, and nomenclature of the SNPs

GeneBin#SNP IDSNPPosition in reference sequencePosition in gene+Position in proteinNotes
CSF21rs2069614T/C69-1916 (promoter)
1rs2069616A/G545-1440 (promoter)Genotyped
1rs1469149A/C1310-675 (promoter)
1rs743564T/C33471363 (third intron)
2rs25881C/T36061622 (third intron)Genotyped as a replacement for 1944
2rs25882T/C39281944 (fourth exon)I117TGenotype failed
2rs25883G/A44002416 (3′ flanking region)
2rs25884A/G47062722 (3′ flanking region)
2rs27438G/A57233739 (3′ flanking region)
CSF31rs2227315A/G28-2012 (promoter)
1rs2227322G/C1980-60 (promoter)
1rs1042658T/C42152176 (3′ UTR)Genotyped
1rs2512146G/T51683129 (3′ flanking region)
2rs2227319G/A1158-882 (promoter)Genotyped
2rs2227321G/C1607-433 (promoter)
2rs25645G/A34561417 (fifth exon)L185L
2rs2227333C/G44802441 (3′ flanking region)
3rs2227316C/T321-1719 (promoter)Genotyped
3rs2827C/T40502011 (3′ UTR)
  • All SNPs with minor allele frequency >5% are tagSNPs in this example. One SNP was genotyped in each bin. CSF: colony-stimulating factor; UTR: untranslated region. #: sites are ordered by linkage disequilibrium, with sites showing similar patterns of genotype put into the same bin; : position in sequence AF373868 for CSF2 and in sequence AF388025 for CSF3; +: numbered by denoting the first nucleotide of the initiator methionine codon as +1 (position 1,985 in sequence AF373868 of CSF2 and position 2,040 in sequence AF388025 of CSF3).