Prioritized suggestive genome-wide loci based on mice experiments of Likelihood-based Causality Model Selection (LCMS) regulatory network analyses, gene expression signature profiles in osteoblasts, and transcriptome atlas of mouse embryos.

a Suggestive genome-wide significant SNPs: See text for criteria.
b SNP locates within a gene.
*: For the most significantly associated SNP located on the intergenic regions, the closest nearby gene was selected.
c SNP location is shown if SNP locates within a gene. The distance (Kb) from an intergenic SNP to the closest gene is shown if SNP locates in the intergenic regions.
d NL: Neck Length; NW: Neck Width; NSA: Neck Shaft Angle.
e PTH stimulated primary osteoblasts: 0: not expressed; +: expression level < 100 in all 3 replicas; ++: expression level > 100 in all 3 replicas;+++: expressed in all 3 replicas and regulated by PTH. ↑: Up-regulated by PTH; ↓ Down-regulated by PTH.
f ANOVA was used to test the differential expression across 7 time points (Day 4, 5, 6, 8, 16, 25 and 30 post-induction) during osteoblast development. P-value cut off is equal to 4.59E-04 ( = 0.05/109).
g LCMS analysis: Likelihood-based Causality Model Selection. Six bone related traits were tested. For each trait test, at least 2 significant pleiotropy of eQTL and trait QTL was considered evidence for a causally relation to the candidate gene. Detailed results are shown in Table S4.
h RNA in situ hybridization from E14.5 wild type murine embryos. Average expression strength calculated from the assay annotation grouped into 25 subsets of organ/tissue systems of the mouse anatomy. In this table, we only display subsets including 1: Skeleton; 2: Brain and CNS; 3: Spinal cord; 4: PNS; 5: Ganglia; 6:Limb; 7: Skeletal muscle; and 8: Others.
no gene expression is not detectable. n.a.: Expression level is not available, since transcripts are not presented on expression arrays.
e,f,g,h Results of experiments were obtained from different mice strains and different Laboratories.