Table 2.
GWS BMI loci from secondary analyses
| SNP | Chr:position | Notable gene(s)* | Alleles | EAF | β | s.e.m. | P value | Analysis |
|---|---|---|---|---|---|---|---|---|
|
Novel loci
| ||||||||
| rs9641123 | 7:93,035,668 | CALCR(B,N); hsa-miR-653(Q) | C/G | 0.430 | 0.029 | 0.005 | 2.08 × 10−10 | EPB |
| rs7164727 | 15:70,881,044 | LOC100287559(N), BBS4(B,M,Q) | T/C | 0.671 | 0.019 | 0.003 | 3.92 × 10−9 | All |
| rs492400 | 2:219,057,996 |
PLCD4(B,Q); CYP27A1(B); USP37(N); TTLL4(M,Q); STK36(B,M); ZNF142(M); RQCD1(Q) |
C/T | 0.424 | 0.024 | 0.004 | 6.78 × 10−9 | Men |
| rs2080454 | 16:47,620,091 | CBLN1(N) | C/A | 0.413 | 0.017 | 0.003 | 8.60 × 10−9 | All |
| rs7239883 | 18:38,401,669 | LOC284260(N); RIT2(B,D) | G/A | 0.391 | 0.023 | 0.004 | 1.51 × 10−8 | Women |
| rs2836754 | 21:39,213,610 | ETS2(N) | C/T | 0.599 | 0.017 | 0.003 | 1.61 × 10−8 | All |
| rs9914578 | 17:1,951,886 | SMG6(D,N); N29617(Q) | G/C | 0.229 | 0.020 | 0.004 | 2.07 × 10−8 | All |
| rs977747 | 1:47,457,264 | TAL1(N) | T/G | 0.403 | 0.017 | 0.003 | 2.18 × 10−8 | All |
| rs9374842 | 6:120,227,364 | LOC285762(N); | T/C | 0.744 | 0.023 | 0.004 | 2.67 × 10−8 | EPB |
| rs4787491 | 16:29,922,838 |
MAPK3(D); KCTD13(D); INO80E(N); TAOK2(D); YPEL3(D); DOC2A(D); FAM57B(D) |
G/A | 0.510 | 0.022 | 0.004 | 2.70 × 10−8 | EPB |
| rs1441264 | 13:78,478,920 | MIR548A2(N) | A/G | 0.613 | 0.017 | 0.003 | 2.96 × 10−8 | All |
| rs17203016 | 2:207,963,763 | CREB1(B,N); KLF7(B) | G/A | 0.195 | 0.021 | 0.004 | 3.41 × 10−8 | All |
| rs16907751 | 8:81,538,012 | ZBTB10(N) | C/T | 0.913 | 0.047 | 0.009 | 3.89 × 10−8 | Men |
| rs13201877 | 6:137,717,234 | IFNGR1(N); OLIG3(G) | G/A | 0.140 | 0.024 | 0.004 | 4.29 × 10−8 | All |
| rs9540493 | 13:65,103,705 | MIR548X2(N); PCDH9(D) | A/G | 0.452 | 0.021 | 0.004 | 4.97 × 10−8 | EPB |
| rs1460676 | 2:164,275,935 | FIGN(N) | C/T | 0.179 | 0.021 | 0.004 | 4.98 × 10−8 | All |
| rs6465468 | 7:95,007,450 | ASB4(B,N) | T/G | 0.306 | 0.025 | 0.005 | 4.98 × 10−8 | Women |
|
| ||||||||
| Previously identified loci | ||||||||
|
| ||||||||
| rs6091540 | 20:50,521,269 | ZFP64(N) | C/T | 0.721 | 0.030 | 0.004 | 2.15 × 10−11 | Women |
| rs7715256 | 5:153,518,086 | GALNT10(N) | G/T | 0.422 | 0.017 | 0.003 | 8.85 × 10−9 | All |
| rs2176040 | 2:226,801,046 | LOC646736(N); IRS1(B,Q) | A/G | 0.365 | 0.024 | 0.004 | 9.99 × 10−9 | Men |
SNP positions are reported according to Build 36 and their alleles are coded based on the positive strand. Alleles (effect/other), EAF, beta (β), s.e.m. and P values are based on the meta-analysis of GWAS I + II+ Metabochip association data from the data set shown in the ‘Analysis’ column. EPB denotes European population-based studies, ‘All’ denotes all ancestries.
*
Notable genes from biological relevance to obesity (B); copy number variation (C); DEPICT analyses (D); GRAIL results (G); BMI-associated variant is in strong LD (r2 ≥ 0.7) with a missense variant in the indicated gene (M); gene nearest to the index SNP (N); association and eQTL data converge to affect gene expression (Q).