Connecting phenotypic variation (QTL) to a candidate quantitative trait gene (QTG) and putative quantitative trait nucleotide (QTN). A and B: Variation in tibia length (mm) between LG and SM mapped to a QTL on chromosome 6. C: This QTL was localized to a genomic region and intersected with LG/J, SM/J SNPs and IBD regions. D: SNPs falling in non-IBD regions were interrogated and a SNP falling in exon 14 of Ptprz1, which affects bone-growth, was identified. The SNP changes the encoded amino acid from proline to histidine. E: This amino acid is 100% IBD and the amino acid variant occurs in SM/J and one other unrelated strain of laboratory mouse, NZO/HlLtJ. This SNP is predicted to be functionally damaging by the LRT, PolyPhen-2 and SIFT algorithms, and represents a fruitful candidate QTN for further functional follow-up.