Table 1.
Coding ABO Variants Identified in Finnish Probands with Otitis Media
| chr:pos_ref/alt (hg19) | rsID | Varianta | GTEx eQTL tissueb | GTEx eQTL p-value | gnomAD Finnish allele count | gnomAD Finnish allele number | gnomAD Finnish MAF | n Finnish proband carriers (%)c | Blood type: n (%)d |
|---|---|---|---|---|---|---|---|---|---|
| 9:136131056_CG/C | 56392308 | c.1061delC(p.Pro354Argfs*) | NA | NA | 2381 | 22672 | 0.105 | 11 (28) | A: 10 (91) |
| 9:136131289_C/T | 8176748 | c.829G>A(p.Val277Met) | Esophagus-mucosa | 3.8 × 10−21 | 4427 | 24872 | 0.178 | 13 (32) | A: 7 (54) |
| 9:136131315_C/G | 8176747 | c.803G>C(p.Gly268Ala) | Lung | 1.5 × 10−43 | 3375 | 24602 | 0.137 | 10 (25) | B: 8 (80)/AB: 2 (20) |
| 9:136131322_G/T | 8176746 | c.796C>A(p.Leu266Met) | Lung | 1.5 × 10−43 | 3361 | 24576 | 0.137 | 10 (25) | B: 8 (80)/AB: 2 (20) |
| 9:136131415_C/T | 8176743 | c.703G>A(p.Gly235Ser) | Lung | 1.5 × 10−43 | 2935 | 21424 | 0.137 | 10 (25) | B: 8 (80)/AB: 2 (20) |
| 9:136131472_A/T | 8176740 | c.646T>A(p.Phe216Ile) | Esophagus-mucosa | 6.7 × 10−21 | 3804 | 21946 | 0.198 | 13 (32) | A: 7 (54) |
| 9:136131523_G/A | 8176739 | c.595C>T(p.Arg199Cys) | NA | NA | 255 | 23488 | 0.011 | 2 (5) | A: 2 (100) |
| 9:136131592_G/C | 7853989 | c.526C>G(p.Arg176Gly) | Lung | 1.3 × 10−36 | 3884 | 24828 | 0.156 | 10 (25) | B: 8 (80)/AB: 2 (20) |
| 9:136131651_G/A | 1053878 | c.467C>T(p.Pro156Leu) | Lung | 1.6 × 10−07 | 2748 | 24962 | 0.110 | 11 (28) | A: 10 (91) |
| 9:136132908_T/TC | 8176719 | c.260insG(p.Val87_Thr88fs*) | Esophagus-mucosa | 4.8 × 10−45 | 11730 | 24958 | 0.470 | 36 (90)e | Wt 7, O: 7 (100); Het 22, A: 14 (64); Hom 11, A: 9 (82)/AB: 2 (18)f |
| 9:136133506_A/G | 512770 | c.220C>T(p.Pro74Ser) | Esophagus-mucosa | 1.0 × 10−12 | 21136 | 24894 | 0.849 | 40 (100) | A: 23 (58) |
| 9:136135238_T/C | 549446 | c.188G>A(p.Arg63His) | Esophagus-mucosa | 3.0 × 10−20 | 20513 | 24972 | 0.821 | 13 (32) | A: 7 (54) |
| 9:136136770_A/C | 688976 | c.106G>T(p.Val36Phe) | Esophagus-mucosa | 1.4 × 10−19 | 19220 | 23386 | 0.822 | 40 (100) | A: 23 (58) |
| 9:136136773_C/T | 8176696 | c.103G>A(p.Gly35Arg) | NA | NA | 473 | 23194 | 0.020 | 4 (10) | A: 2 (50) |
Variants that are primary determinants of blood type are in bold.
Top epithelial tissue in eQTL list for variant according to smallest p-value.
Counts and proportions out of 40 Finnish probands with blood types and exome data. Variants with similar counts are in strong linkage disequilibrium, for example, the 4-variant haplotype comprising variants [c.526C>G (p.Arg176Gly); c.703G>A (p.Gly235Ser); c.796C>A (p.Leu266Met); c.803G>C (p.Gly268Ala)] is carried by the same 10 probands who all express B antigen.
Counts and proportions out of variant carriers in previous column. The blood types shown are based on majority counts for each variant. If carriers of the four-variant haplotype that confers type B and individuals who are wild type for the c.260insG (p.Val87_Thr88fs*) with blood type O are excluded, all remaining probands with available blood types are type A. Two probands who are type AB are both heterozygous for the four-variant haplotype and homozygous for the c.260insG variant.
Blood type O or A antigen expression depends on genotype for the c.260insG variant: wild type individuals are type O, whereas homozygous individuals have A antigen.
Proportions reported are based on genotype for the c.260insG variant.
eQTL, expression quantitative trait loci; GTEx, Genotype-Tissue Expression database.