Table 2.
Associated variants with hematuria in genome-wide association studies followed by conditional regional analysis at each locus
| Chromosome:Position | Reference/ Alternate Allele | rs Identification | Nearest Gene(s) and Location | Minor Allele Frequency (Minor Allele) | P Value | Odds Ratio (95% Confidence Interval) | Imputation Quality |
|---|---|---|---|---|---|---|---|
| GRCh37 | |||||||
| 1:13,921,934 | A/G | rs2885134 | PDPN (intron 1) | 0.029 (G) | 5.90E-9 | 1.22 (1.14 to 1.31) | 0.958 |
| HLA-B*0801 | — | — | — | 0.14 | 4.41E-19 | 0.84 (0.82 to 0.88) | N/A |
| 11:121,584,573 | T/A | rs618048 | SORL1 (downstream 3′) | 0.22 (T) | 1.30E-11 | 0.91 (0.88 to 0.94) | 0.999 |
| 19:41,826,020 | A/C | rs56254331 | CCDC97 (intron 3), TGFB1 (downstream 3′) | 0.17 (C) | 8.80E-16 | 0.89 (0.86 to 0.91) | 0.999 |
| 16:57,349,346 | G/T | rs948705 | PLLP (intergenic with CCL22) | 0.15 (G) | 2.30E-9 | 1.10 (1.07 to 1.14) | 0.976 |
| GRCh38 | |||||||
| chr2:227052367 (most significant variant in locus) | G/C | rs35138315 | COL4A4 (p.Ser969x, exon 32) | 0.00035 (C) | 7.95E-35 | 87.3 (47.9 to 159.0) | 0.567 |
| chr2:227077364 (results conditioned on rs35138315) | T/C | rs58261427 | COL4A4 (intron 25) | 0.214 (C) | 2.00E-9 | 1.09 (1.06 to 1.12) | 0.987 |
| chr2:227277511 (results conditioned on rs35138315) | G/A | rs200287952 | COL4A3 (p.Gly695Arg, exon 28) | 0.00021 (A) | 2.16E-7 | 45.5 (11.8 to 168.0) | 0.268 |
For GRCh37, a genome-wide association study was performed using centrally Haplotype Reference Consortium–imputed UK Biobank data, in which variants are reported in reference to GRCh37. After conditioning on the most significant variant at each locus, all other associations in the region became nonsignificant. For GRCh38, reimputation of a 2-Mb region encompassing COL4A4-COLA43 was performed using the Trans-Omics for Precision Medicine Program (reference GRCh38) followed by conditional regional analysis to identify independent associated variants. Reported odds ratios refer to the alternate allele.