SNPs showing significant association with aGVHD
| Locus . | Genes in LD block . | Analysis type . | Most significant SNP in the region . | Test statistics in GWAS . | Competing risk regression analysis among the entire cohort . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Log-rank test . | Log-rank trend test . | |||||||||||||
| Subject* . | Event . | db SNP ID . | Position (hg19) . | Allele (frequency†, %) . | Mismatch frequency‡ (among the entire cohort), % . | χ2 . | P . | χ2 . | P . | HR (95% CI) . | P . | |||
| 6p21.32 | HLA-DPB1, HLA-DPA1 | All | II-IV aGVHD | rs6937034 (On chip) | 33 079 766 | A/G (32.3) | 26.5 (—) | 37.5 | 9.06 × 10−10 | 29.1 | 6.76 × 10−8 | 1.65 (1.40-1.95) | 4.50 × 10−9 | |
| 12p12.1 | KRAS, LYRM5, CASC1, LRMP | DQB1 | *06:01 | III-IV aGVHD | rs17473423 (On chip) | 25 362 777 | A/G (13.1) | 20.5 (10.2) | 37.5 | 9.34 × 10−10 | 48.9 | 2.73 × 10−12 | 2.44 (1.88-3.15) | 1.20 × 10−11 |
| B | *52:01 | C/T (13.1) | 19.7 (7.6) | 34.4 | 4.42 × 10−9 | 45.1 | 1.87 × 10−11 | 2.48 (1.88-3.26) | 8.40 × 10−11 | |||||
| C | *12:02 | rs7976254 (On chip) | 25 256 354 | C/T (13.1) | 19.7 (7.6) | 34.4 | 4.42 × 10−9 | 45.1 | 1.87 × 10−11 | 2.48 (1.88-3.26) | 8.40 × 10−11 | |||
| DRB1 | *15:02 | C/T (13.0) | 19.8 (7.4) | 32.5 | 1.20 × 10−8 | 43.0 | 5.47 × 10−11 | 2.47 (1.87-3.25) | 1.40 × 10−10 | |||||
| 9q31.3 | None | B | *44:03 | III-IV aGVHD | rs9657655 (Imputed) | 113 391 486 | A/T (5.4) | 12.3 (2.5) | 38.0 | 7.00 × 10−10 | 33.1 | 8.79 × 10−9 | 3.31 (2.02-5.42) | 2.10 × 10−6 |
| C | *14:03 | A/T (5.4) | 12.3 (2.5) | 38.0 | 7.00 × 10−10 | 33.1 | 8.79 × 10−9 | 3.31 (2.02-5.42) | 2.10 × 10−6 | |||||
| A | *33:03§ | A/T (5.3) | 13.2 (2.7) | 32.1 | 1.46 × 10−8 | 28.2 | 1.09 × 10−7 | 3.29 (2.03-5.32) | 1.30 × 10−6 | |||||
| 6q16.2 | None | C | *07:02 | III-IV aGVHD | rs12206927 (Imputed) | 99 613 136 | A/G (9.6) | 11.% (2.5) | 33.5 | 6.97 × 10−9 | 31.2 | 2.34 × 10−8 | 3.68 (2.40-5.64) | 2.50 × 10−9 |
| Locus . | Genes in LD block . | Analysis type . | Most significant SNP in the region . | Test statistics in GWAS . | Competing risk regression analysis among the entire cohort . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Log-rank test . | Log-rank trend test . | |||||||||||||
| Subject* . | Event . | db SNP ID . | Position (hg19) . | Allele (frequency†, %) . | Mismatch frequency‡ (among the entire cohort), % . | χ2 . | P . | χ2 . | P . | HR (95% CI) . | P . | |||
| 6p21.32 | HLA-DPB1, HLA-DPA1 | All | II-IV aGVHD | rs6937034 (On chip) | 33 079 766 | A/G (32.3) | 26.5 (—) | 37.5 | 9.06 × 10−10 | 29.1 | 6.76 × 10−8 | 1.65 (1.40-1.95) | 4.50 × 10−9 | |
| 12p12.1 | KRAS, LYRM5, CASC1, LRMP | DQB1 | *06:01 | III-IV aGVHD | rs17473423 (On chip) | 25 362 777 | A/G (13.1) | 20.5 (10.2) | 37.5 | 9.34 × 10−10 | 48.9 | 2.73 × 10−12 | 2.44 (1.88-3.15) | 1.20 × 10−11 |
| B | *52:01 | C/T (13.1) | 19.7 (7.6) | 34.4 | 4.42 × 10−9 | 45.1 | 1.87 × 10−11 | 2.48 (1.88-3.26) | 8.40 × 10−11 | |||||
| C | *12:02 | rs7976254 (On chip) | 25 256 354 | C/T (13.1) | 19.7 (7.6) | 34.4 | 4.42 × 10−9 | 45.1 | 1.87 × 10−11 | 2.48 (1.88-3.26) | 8.40 × 10−11 | |||
| DRB1 | *15:02 | C/T (13.0) | 19.8 (7.4) | 32.5 | 1.20 × 10−8 | 43.0 | 5.47 × 10−11 | 2.47 (1.87-3.25) | 1.40 × 10−10 | |||||
| 9q31.3 | None | B | *44:03 | III-IV aGVHD | rs9657655 (Imputed) | 113 391 486 | A/T (5.4) | 12.3 (2.5) | 38.0 | 7.00 × 10−10 | 33.1 | 8.79 × 10−9 | 3.31 (2.02-5.42) | 2.10 × 10−6 |
| C | *14:03 | A/T (5.4) | 12.3 (2.5) | 38.0 | 7.00 × 10−10 | 33.1 | 8.79 × 10−9 | 3.31 (2.02-5.42) | 2.10 × 10−6 | |||||
| A | *33:03§ | A/T (5.3) | 13.2 (2.7) | 32.1 | 1.46 × 10−8 | 28.2 | 1.09 × 10−7 | 3.29 (2.03-5.32) | 1.30 × 10−6 | |||||
| 6q16.2 | None | C | *07:02 | III-IV aGVHD | rs12206927 (Imputed) | 99 613 136 | A/G (9.6) | 11.% (2.5) | 33.5 | 6.97 × 10−9 | 31.2 | 2.34 × 10−8 | 3.68 (2.40-5.64) | 2.50 × 10−9 |
LD, linkage disequilibrium.
“All” refers to no stratification being applied; subsequent entries in this column were DPB1 allele mismatch stratified.
Frequency of the second listed allele.
Genotype mismatch frequency in GVH direction.
For each locus, all the results from the same group indicated in supplemental Table 1 were listed in this table, if they were not significant.