Table 1 Summary of results from enrichment analysis of ΔAF > 0.8 SNPs located in conserved noncoding elements.

One significantly enriched term was chosen from each group of significantly enriched intercorrelated terms. Full lists of enriched terms and intercorrelations are presented in database S3, and the most enriched intercorrelated terms are presented in fig. S5. P values are Bonferroni-corrected. O/R, number of distinct nonoverlapping 1-Mb windows observed (O) and the average number of 1-Mb windows observed in 1000 random (R) samplings of the same number of genes (rounded to the nearest integer). TS, Thieler stage.

Database entryEnriched termNumber of genesPEnrichmentDistinct loci (O/R)
Gene Ontology biological process
GO:0007399Nervous system
development
1913.7 × 10–101.7154/155
GO:0045595Regulation of
cell differentiation
1074.5 × 10–61.894/91
GO:0045935Positive regulation of
nucleobase-containing
compound metabolic
process
1222.0 × 10–51.7101/100
GO:0045165Cell fate commitment365.5 × 10–52.931/32
GO:0007389Pattern specification
process
571.4 × 10–42.243/44
GO:0009887Organ morphogenesis852.0 × 10–31.872/73
GO:0048646Anatomical structure
formation involved
in morphogenesis
752.8 × 10–31.865/64
GO:0045892Negative regulation
of transcription,
DNA-dependent
821.4 × 10–21.762/62
GO:0034332Adherens junction
organization
131.5 × 10–24.711/11
Mouse Genome Informatics gene expression
11853TS23 diencephalon,
lateral wall,
mantle layer
1093.9 × 10–253.386/85
12449TS23 medulla
oblongata, lateral
wall, basal plate,
mantle layer
1152.6 × 10–132.390/89
2257TS17 sensory organ1133.4 × 10–132.398/99
1324TS15 future brain728.5 × 10–92.461/61
Mouse Genome Informatics phenotype
MP:0010832Lethality during
fetal growth
through weaning
2407.5 × 10–171.8197/189
MP:0003632Abnormal nervous
system morphology
2371.2 × 10–131.7191/193
MP:0005388Respiratory system
phenotype
1271.7 × 10–71.8101/102
MP:0000428Abnormal craniofacial
morphology
1091.4 × 10–61.993/92
MP:0002925Abnormal
cardiovascular
development
883.3 × 10–51.973/73
MP:0005377Hearing/vestibular/ear
phenotype
731.8 × 10–42.061/62