Table 3.
Large (>1000kb) rare deletions.
| Chr:bp-bp | Mb | Cat=N | Immune phenotype | Mapped genes | GWAS Ref. |
|---|---|---|---|---|---|
| 2:25185405-26797358 | 1.61 | U=1 | 1. Type 1 diabetes 2. Lymphocyte counts |
EFR3B DNMT3A |
1. Study GCST001255 (Bradfield, J. P. et al., 2011) 2. Study GCST004627 (Astle, W. J. et al., 2016) |
| 2:106874835-108440432 | 1.57 | U=1 | 1.Serum immune | EEF1A1P12, ST6GAL2 | 1. Study GCST010146 (Zhang, R. et al., 2020). |
| 2:111399346-113093928 | 1.69 | A=1 | 1.Vitiligo 2. Alopecia areata 3. Multiple Sclerosis 4. Systemic Lupus Erythematosus 5. Type 1 diabetes |
MIR4435-2HG ACOXL MERTK BCL2L11, MIR4435-2HG ACOXL |
1. Study GCST004785 (Jin, Y. et al., 2016) 2. Study GCST004866 (Betz, R. C. et al., 2015) 3. Study GCST009597 (International Multiple Sclerosis Genetics Consortium, 2019) 4. Study GCST011956 (Yin, X. et al., 2021) 5. Study GCST005536 (Onengut-Gumuscu, S. et al., 2015) |
| 2:122785624-125774467 | 2.56 | A=1 U=1 |
None | ||
| 3:1632353-2788576 | 1.16 | U=1 | 1. Serum immune biomarker levels | CNTN4 | 1. Study GCST010146 (Zhang, R. et al., 2020) |
| 3:144445174-145758050 | 1.31 | A=1 | None | ||
| 3:174910449-176153637 | 1.24 | U=1 | None | ||
| 4:188917331-190459134 | 1.54 | U=1 | None | ||
| 5:24837197-26174342 | 1.34 | A=1 | None | ||
| 5:19293784-20970950 | 1.68 | A=1 | None | ||
| 8:28935001-30828160 | 1.89 | A=1 | 1. Lymphocyte count | RBPMS-AS1, TUBBP1 | 1. Study GCST90002320 (Chen, M.-H. et al., 2020); and study GCST90002388 (Vuckovic, D. et al., 2020) |
| 13:56798769-57813567 | 1.01 | A=1 U=1 |
None | ||
| 13:55968185-57432964 | 1.46 | A=1 | None | ||
| 13:80959100-82030660 | 1.07 | A=1 | None | ||
| 16:15125441-16305355 | 1.18 | A=1 U=2 |
1. Serum immune biomarker levels | NDE1, MYH11 | 1. Study GCST010146 (Zhang, R. et al., 2020) |
| 17:14098277-15430857 | 1.31 | A=2 | 1. Lymphocyte count | PMP22, TEKT3 | 1. Study GCST011881 (1. Okada, D. et al., 2021) |
| 18:63697503-66099958 | 2.40 | A=1 | None | ||
| 21:22668119-25713704 | 3.05 | U=1 | None |
Chr:bp-bp - deletion coordinates; GRCh37; Mb - length of deletion in megabases. Cat=N - category in which deletion found; and number in each category; A = affected with Addison’s; U = unaffected; Immune phenotype - reported immune-related phenotype for which there is a genome-wide significantly associated locus falling within the deletion (source: GWAS catalog); Mapped genes - Gene(s) mapped to the strongest SNP as listed in GWAs catalog. If the SNP is located within a gene; that gene is listed. If the SNP is located within multiple genes; these genes are listed separated by commas. If the SNP is intergenic; the upstream and downstream genes are listed; separated by a hyphen (from GWAS Catalog documentation); GWAS Ref. - reference to the relevant GWAS. Deletion with majority overlapping coordinates have been merged; to cover their cumulative greatest extent.
Underline words means Case-deletions covering regions of GWAS-association to immune diseases.