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Fig. 1 | Genome Medicine

Fig. 1

From: High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing

Fig. 1

The segment structure of GRCh38 3q29 region and haplotypes identified in this study. a 3q29 locus with SDA, SDB, SDC, OMIM Gene Phenotypes, ClinGen Dosage Sensitivity Map—Haploinsufficiency, ClinGen Dosage Sensitivity Map—Triplosensitivity, ClinVar Variants, ClinVar SNVs, and Segmental Duplications are represented as Tracks. The 3q29 GRCh38 in silico map is represented in the last track. ClinVar Track: red dots, pathogenic; dark blue dots, variants of uncertain significance; green dots, benign variants. b 3q29 segments of GRCh38 and T2T with SDA, SDB, and SDC represented as black boxes on top overlaid on the in silico maps (white background with vertical blue lines). Dashed line: the unique region between SDB and SDC. Black arrows in panels a and b—the region included in our analyses. c The structure and prevalence of 13 known haplotypes identified among our samples (H1-H9, H13, H15-H17) and 18 novel haplotypes, which were ordered by frequency (H19-H36). Each colored arrow represents 3q29 segments. Partial, partial copy of 32q9 segments; CNV, copy number polymorphism; INV, inversion. d Prevalence of the 3q29 haplotypes represented in unaffected individuals. e Cohen-Friendly association plot depicting the relationship between haplotypes and populations. If the observed count is greater than expected, the rectangle rises above the baseline and is colored in blue. If the observed count is less than expected, the rectangle falls below the baseline and is colored in red

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