Table 3 Independent replication results for the seven identified index variants in EA populations and evaluation among African Americans.
Index SNP Information | Replication, Metabolite GWAS | Replication, SHIP | Meta-analysis | Look-up, ARIC AA | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Locus* | Variant ID | A1/A2 | Repl SNP | R2 with index SNP§ (D’) | Effect¶ (SE) | P | Effect¶ (SE) | P | Z-score | P | AF | Effect (SE) | P |
EFNA1/SLC50A1 | rs9330264 | T/C | No good proxy, 500 kb region does not contain suggestive association signals | 0.003 (0.01) | 0.8 | 6.02 | 1.78 × 10−9 | 0.09 | 0.27 (0.35) | 0.43 | |||
MCM6/LCT | rs182549 | C/T | rs4988235 | 1 (1) | −0.04 (0.003) | 4.23 × 10−28 | −0.07 (0.01) | 8.93 × 10−8 | -16.91 | 3.72 × 10−64 | 0.88 | −1.32 (0.27) | 8.51 × 10−7 |
SI | rs9825346 | G/A | rs9825346 | 1 (1) | −0.02 (0.003) | 8.18 × 10−9 | −0.03 (0.01) | 0.02 | -8.41 | 4.07 × 10−17 | 0.47 | −0.32 (0.18) | 0.08 |
MGAM | rs11976181 | T/C | rs11976181 | 1 (1) | 0.03 (0.01) | 6.00 × 10−4 | 0.05 (0.02) | 5.95 × 10−3 | 9.96 | 2.36 × 10−23 | 0.26 | −0.24 (0.20) | 0.22 |
MGAM2 | rs13229622# | C/G | Not investigated due to lack of conditional estimates | −0.04 (0.01) | 0.01 | −6.95 | 3.73 × 10−12 | NA | NA | NA | |||
SLC5A10 | rs117355297 | T/C | No good proxy, 500 kb region contains association signal (rs2305062, P = 1.41 × 10−5) | −0.08 (0.03) | 0.01 | −8.52 | 1.62 × 10−17 | 0.01 | −2.63 (1.05) | 0.01 | |||
SLC5A1 | rs117086479 | G/A | rs10483162 | 1 (1) | −0.02 (0.005) | 1.52 × 10−5 | −0.05 (0.03) | 0.05 | -7.21 | 5.67 × 10−13 | 0.01 | −1.49 (0.85) | 0.08 |
