Table 2.
VUR associations
| Top SNP | Chr. | Position | Nearest Genes | A1/A2 | Effect Allele (A1) freq. | OR (95% CI) | P | Model |
|---|---|---|---|---|---|---|---|---|
| rs13013890 | 2 | 63,654,109 | WDPCP, MDH1, OTX1, EHBP1, UGP2, VPS54 | A/G | 0.12 | 3.65 (2.39 to 5.56) | 1.86×10−9 | Recessive |
| rs10806089 | 6 | 77,943,057 | HTR1B | C/T | 0.34 | 2.75 (1.96 to 3.84) | 4.10×10−9 | Recessive (males) |
| rs1154855 | 6 | 55,612,107 | BMP5 | G/T | 0.48 | 1.41 (1.26 to 1.59) | 4.33×10−9 | Additive (females) |
| rs76292820 | 8 | 19,313,619 | CSGALNACT1 | T/C | 0.16 | 4.71 (2.72 to 8.17) | 3.46×10−8 | Recessive (males) |
| rs12759898 | 1 | 116,351,384 | NHLH2, VANGL1, CASQ2 | A/T | 0.08 | 1.61 (1.36 to 1.9) | 3.56×10−8 | Dominant |
| rs16838525 | 1 | 195,509,949 | AL357932.1 | C/T | 0.15 | 6.94 (3.43 to 14.06) | 7.21×10−8 | Recessive (males) |
| rs79060316 | 8 | 81,827,316 | ZNF704, PAG1 | T/C | 0.02 | 2.50 (1.79 to 3.50) | 9.07×10−8 | Dominant |
| rs503022 | 3 | 55,491,436 | WNT5A | A/C | 0.13 | 1.81 (1.45 to 2.25) | 1.19×10−7 | Additive (males) |
Top SNP each locus is shown (dbSNP 151). Positions are in University of California Santa Cruz hg19 coordinates. P values, ORs, and their 95% CIs are derived from meta-analysis of seven European ancestry cohorts (1395 VUR patients and 5366 controls; detailed counts per cohort are shown in Supplemental Table 4), under the indicated models. Chr., chromosome; freq., frequency; WDPCP, WD Repeat Containing Planar Cell Polarity Effector; MDH1, Malate Dehydrogenase 1; OTX1, Orthodenticle Homeobox 1; EHBP1, EH Domain Binding Protein 1; UGP2, UDP-Glucose Pyrophosphorylase 2; VPS54, Vacuolar Protein Sorting-Associated Protein 54; HTR1B, 5-Hydroxytryptamine Receptor 1B; BMP5, Bone Morphogenetic Protein 5; CSGALNACT1, Chondroitin Sulfate N-Acetylgalactosaminyltransferase 1; NHLH2, Nescient Helix-Loop-Helix 2; VANGL1, Vang Gogh-like Planar Cell Polarity Protein 1; CASQ2, Calsequestrin 2; ZNF704, Zinc Finger Protein 704; PAG1, Phosphoprotein Membrane Anchor With Glycosphingolipid Microdomains 1; WNT5A, Wnt Family Member 5A.