IGV visualization of the read alignment and assembly of rs1140458 region for three illustrative RPE samples. Top. Sequencing reads with variant (A, in green) and reference nucleotide at the SNP position in the proximity of an exon-intron boundary are shown. Variant-harboring reads often continue in the intron, indicating association with potential junction alteration. Bottom. Cufflinks assembly (.gtf) showing the presence of an isoform retaining the intron 18 of the NPC1 gene (ENST00000540608 represents spliced isoform, and ENST0000269228 represents intron-retaining isoform.