The best replacement for snp is mutation.

The best alternatives to snp are rated as following:
★★★★★  mutation
★★★★  snv
★★★  cnv
★★★  rflp
★★  str
★★  microsatellite
★★  cgh array
★  point mutation
★  ukip
★  cgh
★  gtn
  haplotype
  ntg

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