Suzanne de Bruijn

270 Chapter 5 Table S7. Rare genetic variants located within the CEVA haplotype Genome RefSNP Location gnomAD AF (%) SpliceAI PhyloP Repeatmasker Regulatory element Chr7:106622156T>A rs6961007 Intergenic - NA -5.094 SINE - Chr7:106669858G>A ( SNP1 ) rs17424561 Intergenic 3.04 NA -1.806 - - Chr7:106690778CTTTT>T NA Intronic ( PPKAR2B ) - 0.01 0.556 - - Chr7:106736863C>T rs149440050 Intronic ( PPKAR2B ) 3.07 0.01 0.135 LINE - Chr7:106741374T>C ( SNP2 ) rs79579403 Intronic ( PPKAR2B ) 3.03 0.00 0.8 LINE GeneHancer Chr7:106741580ATT>A NA Intronic ( PPKAR2B ) - 0.01 0 LINE GeneHancer Chr7:106764419T>A ( SNP3 ) rs17425867 Intronic ( PPKAR2B ) 3.05 0.00 0.852 - - Chr7:106807591TAAAA>T NA Intergenic - NA 0.621 - - Chr7:106812322A>AA NA Intronic ( HBP1 ) - 0.00 -2.377 SINE - Chr7:106815154T>C ( SNP4 ) rs117113959 Intronic ( HBP1 ) 2.93 0.05 -0.481 - - Chr7:106837681G>A ( SNP5 ) rs17349280 Intronic ( HBP1 ) 2.90 0.01 0.275 - - Chr7:106930234C>T ( SNP6 ) rs117386523 Intronic ( COG5 ) 2.92 0.00 0.641 - - Chr7:106967931A>G ( SNP7 ) rs80149210 Intronic ( COG5 ) 2.91 0.00 0.838 LINE - Chr7:106993159AT>A ( SNP8 ) rs199667576 Intronic ( COG5 ) 2.96 0.00 -100 - - Chr7:107014419A>G ( SNP9 ) rs9649298 Intronic ( COG5 ) 2.90 0.00 2.769 - - Chr7:107081658G>A rs188905420 Intronic ( COG5 ) 2.31 0.00 -2.019 SINE - Chr7:107147622T>C ( SNP10 ) rs117714350 Intronic ( COG5 ) 2.32 0.00 0.238 LINE - Chr7:107242636CT>C ( SNP11 ) rs199915614 Intronic ( BCAP29 ) 1.91 NA -100 - - Chr7:107282469A>C ( SNP12 ) rs150942317 Intergenic 2.31 NA 0.241 LTR - Chr7:107316164G>A rs185507318 Intronic ( SLC26A4 ) 2.01 0.00 0.089 SINE - Rare genetic variants (allele frequency ≤5% gnomAD) that are shared between two individuals that harbor the CEVA allele. SNPs that are part of the previously described CEVA (SNP 1-12) or the V1-CEVA haplotype (SNP 4-12) are underlined. Genome, Genomic position according to GRCh37/hg19; RefSNP, dbSNP reference SNP number; GnomAD AF, allele frequency (%) in gnomAD database V.2.1.1; spliceAI, highest splicing prediction score; RepeatMasker, the interspersed repeats or low complexity DNA sequence at the genomic position according to RepeatMasker; Regulatory element, overlap of the genomic position with a predicted cis regulatory element according to GeneHancer V5 or EnhancerAtlas 2.0; NA, not available.