Fig. 1

Genomic distribution of nsCL/P risk-associated SNPs (A) Schematic of linkage disequilibrium (LD) SNP compilation from the GWAS catalog. ASN, Asian; EUR, European. (B and C) Pie chart showing the distribution of nsCL/P AVS across the genome in MiTranscriptome (B) and the GENCODE (C). (D) Genomic regulatory element and GWAS overlap algoRithm (GREGOR) enrichment analyses of the nonsyndromic cleft lip with/without cleft palate (nsCL/P)-associated variant set (AVS) in different genomic regions. The dashed line represents p = 0.05. (E and F) Enrichment of nsCL/P AVS in various histone modifications (E) and chromatin state segmentations (F) at different Carnegie stages (CSs) was assessed using GREGOR. (G) Enrichment of AVS at different transcription factor-binding sites in embryonic stem cells; red dots represent transcription factors with p < 0.05. (H) Number of transcription factor (TF)-binding motifs disrupted by nsCL/P risk SNPs (left). Number of TF binding motifs disrupted by functional SNPs that overlap craniofacial DHS peaks (right). The arrows represent the number of nsCL/P AVS that do not alter TF binding motifs. (I) Occupancy matrix of disrupted TF across DHS containing nsCL/P AVS.