Table 4. Interrogation of best SNPs with the smallest p-value within known EA loci in AA for trait WHR ratio adjusted for BMI.
| Best SNP results in AA sample | |||||||||||||||||
| Stage 1 | Stage 2 | Combined | |||||||||||||||
| Genes | Best_SNP | All1 | EAF2 | P-val | beta | SE | N3 | P4 | YRI5 r2 (D′) | CEU5 r2 (D′) | beta | SE | P-val6 | beta | SE | P-val | P2GC 7 |
| SNPs associated with waist-related trait at significant level | |||||||||||||||||
| TBX15-WARS2 | rs10923714 | a/g | 0.29 | 1.8E-04 | 0.04 | 0.01 | 34 | 1.5E-03 | 0.49 (1.00) | 0.48 (1.00) | 0.03 | 0.02 | 6.4E-02 | 0.04 | 0.01 | 6.8E-05 | 1.1E-04 |
| GRB14 | rs13389219 | t/c | 0.71 | 4.7E-05 | −0.05 | 0.01 | 42 | 1.2E-03 | 1.00 (1.00) | 0.93 (1.00) | −0.02 | 0.02 | 2.0E-01 | −0.04 | 0.01 | 9.5E-05 | 1.4E-04 |
| ADAMTS9 | rs13060013 | a/c | 0.22 | 3.9E-05 | 0.05 | 0.01 | 95 | 5.3E-04 | 0.01 (0.45) | 0.33 (1.00) | 0.02 | 0.02 | 1.2E-01 | 0.04 | 0.01 | 3.8E-05 | 5.9E-05 |
| LY86 | rs1294410 | t/c | 0.23 | 6.3E-07 | −0.06 | 0.01 | 130 | 3.8E-04 | 0.39 (0.68) | 0.83 (0.96) | −0.02 | 0.02 | 1.1E-01 | −0.05 | 0.01 | 1.0E-06 | 1.8E-06 |
| RSPO3 | rs1936806 | t/c | 0.29 | 1.1E-04 | 0.04 | 0.01 | 24 | 2.1E-03 | 0.52 (1.00) | 0.88 (1.00) | 0.00 | 0.02 | 4.4E-01 | 0.03 | 0.01 | 8.1E-04 | 1.1E-03 |
| ITPR2-SSPN | rs11048510 | c/g | 0.23 | 5.8E-04 | 0.04 | 0.01 | 88 | 5.7E-04 | 0.00 (0.25) | 0.03 (0.19) | 0.04 | 0.02 | 1.3E-02 | 0.04 | 0.01 | 4.1E-05 | 6.0E-05 |
| Further SNPs evaluated in follow up but not achieving significance in combined analysis | |||||||||||||||||
| LYPLAL1 | rs2791547 | a/t | 0.67 | 2.0E-03 | −0.03 | 0.01 | 51 | 9.8E-04 | 0.00 (0.09) | 0.62 (0.95) | −0.01 | 0.02 | 3.7E-01 | −0.03 | 0.01 | 4.9E-03 | 6.0E-03 |
| NISCH-STAB1 | rs4687612 | a/g | 0.95 | 5.3E-03 | −0.07 | 0.02 | 17 | 2.9E-03 | N/A | 0.01 (1.00) | −0.03 | 0.04 | 2.5E-01 | −0.06 | 0.02 | 6.0E-03 | 7.4E-03 |
| VEGFA | rs1761769 | t/g | 0.30 | 3.1E-04 | −0.05 | 0.01 | 74 | 6.8E-04 | 0.12 (0.70) | 0.00 (0.06) | 0.01 | 0.02 | 2.6E-01 | −0.03 | 0.01 | 5.1E-03 | 6.3E-03 |
| SNP evaluated but not achieving significance in discovery analysis | |||||||||||||||||
| DNM3-PIGC | rs4916264 | t/c | 0.66 | 4.4E-03 | −0.04 | 0.02 | 47 | 1.1E-03 | 0.06 (1.00) | 0.63 (1.00) | |||||||
| CPEB4 | rs2659191 | a/g | 0.88 | 1.2E-02 | 0.04 | 0.02 | 92 | 5.4E-04 | N/A | 0.16 (1.00) | |||||||
| NFE2L3 | rs4719818 | t/g | 0.21 | 2.1E-03 | −0.04 | 0.01 | 56 | 8.9E-04 | 0.04 (0.42) | 0.07 (0.50) | |||||||
| HOXC13 | rs7970400 | t/c | 0.65 | 4.6E-03 | 0.03 | 0.01 | 62 | 8.1E-04 | 0.02 (0.28) | 0.02 (0.17) | |||||||
| ZNRF3-KREMEN1 | rs16987063 | c/g | 0.88 | 1.6E-02 | 0.06 | 0.02 | 47 | 1.1E-03 | 0.01 (0.17) | N/A | |||||||
The index SNPs are from Heid et al, Nature Genetics 2010 [17]. Note that Tables 3 and 4 show different information for the same loci ( Table 3 for index SNP and Table 4 for best SNPs with the smallest p-value).
1
effect allele/other allele.
2
effect allele frequency.
3
number of independent (typed) SNPs interrogated in AA sample.
4
Bonferroni p-value threshold (0.05/N3).
5
HapMAP LD information.
6
one-side test p-value.
7
P2GC: double GC-corrected p-value.