Suzanne de Bruijn

205 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa Table S7. Repetitive elements identified in sequence flanking the breakpoints SV Breakpoint Coordinates Repetitive elements NL-SV1 A-B 57,291,905 97.01% SINE/ALU B-C 57,518,137 24.92% SINE/MIR UK-SV2 D-E 57,275,839 99.34% SINE/ALU E-F 57,456,098 16.28% SINE/ALU F-G 57,468,960 44.19% SINE/ALU G-H 57,559,114 46.18% SINE/ALU SA-SV3 I-J 57,247,615 54.49% SINE/ALU, 39.53% DNA J-K 57,391,678 85.86% SINE/ALU K-L 57,499,214 22.92% SINE/ALU L-M 57,516,678 55.15% SINE/ALU, 14.29% DNA/hAT-Charlie M-N 57,612,711 50.17% SINE/ALU, 20.27% small RNA CA-SV4 O-P 57,233,035 NP P-Q 57,280,008 25.58% SINE/ALU Q-R 57,483,883 NP R-S 57,634,900 96.01% LTR/ERV-class I NL-SV5 T-U 57,260,511 NP U-V 57,515,862 50.17% SINE/ALU, 38.21% LINE/L1 UK-SV6 W-X 57,295,969 72.76% SINE/ALU X-Y 57,510,765 81.06% SINE/ALU UK-SV7 Z-AA AA-AB AB-AC AC-AD 57,259,525 57,453,630 57,468,931 57,710,821 95.68% SINE/ALU 67.11% SINE/ALU 33.22% SINE/ALU 66.45% SINE/ALU UK-SV8 AE-AF 57,277,347 NP AF-AG 57,326,234 NP AG-AH 57,413,153 68.44% SINE/ALU AH-AI 57,631,659 41.86% SINE/ALU, 56.48% LINE/L1 Presence of repetitive elements was assessed using RepeatMasker from the reference sequence, 150 bp reference sequences flanking each side of the breakpoint were used as input. SV, Structural variant; Breakpoint, Breakpoint annotation of genomic regions as illustrated in Figure 2 ; Coordinates, Genomic position of breakpoint according to GRCh37/hg19 coordinates; Repetitive elements. Percentage of repetitive elements present in input sequence per specified element (class/family); NP, Not present.