Table 1. Description of rare copy number variation identified in systemic lupus erythematosus (SLE) patients from the four-step pipeline application.
| Genomic location (GRCh37/hg19) | Genes | Type | Size (Kb) | SLE ID |
Pop freq |
|---|---|---|---|---|---|
| chr1:196964969–196987806 | CFHR5 | Del | 23 | SLE005 | – |
| chr2:34219274–34313413 | – | Del | 94 | SLE009 | < 1% |
| chr2:36932842–36964864 | VIT | Del | 32 | SLE010 | – |
| chr3:65517399–65595008 | MAGI1 | Dup | 78 | SLE015 | < 1% |
| chr5:96625630–96865984 | – | Del | 240 | SLE014 | – |
| chr6:152303218–152311895 | ESR1 | Del | 9 | SLE003 | < 1% |
| chr7:11983316–12078163 | – | Dup | 95 | SLE005 | < 1% |
| chr7:85522989–85709099 | – | Del | 186 | SLE003 | < 1% |
| chr7:114209440–114215739 | FOXP2 | Del | 6 | SLE023 | – |
| chr7:146859536–146868357 | CNTNAP2 | Del | 9 | SLE003 | – |
| chr8:30079990–30202711 | MIR548O2 | Dup | 123 | SLE018 | – |
| chr9:137354612–137529641 | – | Dup | 175 | SLE023 | < 1% |
| chr12:21796951–22445614 | LDHB, KCNJ8, ABCC9, CMAS, ST8SIA1 | Dup | 649 | SLE018 | < 1% |
| chr13:93378273–93386333 | GPC5 | Del | 8 | SLE023 | – |
| chr13:94506273–94515199 | GPC6, GPC6-AS2 | Del | 9 | SLE023 | < 1% |
| chr13:104521177–104647267 | – | Del | 126 | SLE013 | – |
| chr14:67111441–67148873 | GPHN | Dup | 37 | SLE011 | – |
| chr14:67193022–67217571 | GPHN | Del | 25 | SLE016 | < 1% |
| chr22:25066486–25112325 | – | Del | 46 | SLE006 | < 1% |
| chrX:15723836–15831401 | CA5B, INE2, ZRSR2 | Dup | 108 | SLE018 | – |
| chrX:52833688–52904643 | XAGE5, XAGE3 | Dup | 71 | SLE017 | – |
chr = chromosome; Del = deletion; Dup = duplication; ID = identification; Pop freq = population frequency.