Extended Data Table 4. Candidate genes at new loci associated with additional waist and hip-related traits.
Candidate genes for loci shown on Table 3 based on secondary analyses or literature review. Further details are provided in other Supplementary Tables and the Supplementary Note. Loci are shown in order of chromosome and position.
| SNP | Trait | Chr | Locus | Expression QTL (P < 10−5)* | GRAIL (P < 0.05)† | Literature‡ | Other GWAS signals§ | nsSNPs and CNVs (r2> 0.7)∥ |
|---|---|---|---|---|---|---|---|---|
| rs10925060 | WCadjBMI | 1 | OR2W5-NRLP3 | - | - | NLRP3 | - | - |
| rs10929925 | HIP | 2 | SOX11 | - | SOX11 | SOX11 | - | - |
| rs2124969 | WCadjBMI | 2 | ITGB6 | PLA2R1 (SAT) | ITGB6 | - | Idiopathic membranous nephropathy (PLA2R1, LY75, ITGB6: RBMS1) | - |
| rs1664789 | WCadjBMI | 5 | ARL15 | - | - | ARL15 | - | - |
| rs 17472426 | WCadjBMI | 5 | CCNJL | - | - | FABP6 | - | - |
| rs722585 | HIPadjBMI | 6 | GMDS | - | - | - | - | - |
| rs7739232 | HIPadjBMI | 6 | KLHL31 | KLHL31 (SAT) | - | KLHL31-GCLC-ELVOL | - | - |
| rs1144 | WCadjBMI | 7 | SRPK2 | SRPK2 (LCL), MLL5 (Omental) | - | - | - | - |
| rs13241538 | HIPadjBMI | 7 | KLF14 | KLF14 (SAT) | - | KLF14 | HDL cholesterol, Triglycerides, Type 2 diabetes: KLF14 | - |
| rs2398893 | WHR | 9 | PTPDC1 | - | BARX1 | - | - | - |
| rs7044106 | HIPadjBMI | 9 | C5 | - | - | - | - | - |
| rs11607976 | HIP | 11 | MYEOV | - | CCND1 | FGF19-FGF4-FGF3 | - | - |
| rs1784203 | WCadjBMI | 11 | KIAA1731 | - | - | - | - | - |
| rs1394461 | WHR | 11 | CNTN5 | - | - | - | - | - |
| rs319564 | WHR | 13 | GPC6 | - | - | GPC6 | - | - |
| rs4985155 | HIP | 16 | PDXDC1 | PDXDC1 (SAT) | - | PLA2G10-NTAN1 | Femoral neck bone mineral density, Lumbar spine bone mineral density, Plasma phospholipid levels, Metabolic traits, Height: PDXDC1, NTAN1 | NTAN1 (S287P), NTAN1 (H283N) |
| rs2047937 | WCadjBMI | 16 | ZNF423 | - | - | ZNF423-CNEP1R1 | - | - |
| rs2034088 | HIPadjBMI | 17 | VPS53 | VPS53 (Liver, SAT), FAM101B (Omental, SAT) | - | - | - | - |
| rs1053593 | HIPadjBMI | 22 | HMGXB4 | TOM1 (PBMC), HMGXB4 (Blood, SAT) | - | HMGXB4 | - |
HMGXB4 (G165V), CNVR8147.1 |
Gene transcript levels associated with SNP genotype (expression QTL) in the indicated tissue(s).
Genes in pathways identified as enriched by GRAIL analysis.
Strongest candidate genes identified based on manual literature review.
Traits associated at P < 5 × 10−8 in GWAS lookups or in the GWAS catalog using the index SNP or a proxy in high linkage disequilibrium (LD) (r2 > 0.7), and the genes(s) named in those reports.
Nonsynonymous variants (nsSNPs) and copy number variants (CNVs) with tag SNPs in high LD with index SNP based on a 1000 Genomes CEU reference panel. DEPICT analysis was not performed for loci associated with these traits. Chr, Chromosome; WCadjBMI, waist circumference adjusted for body mass index (BMI); HIPadjBMI, hip circumference adjusted for BMI; WHR, waist-to-hip ratio.