Table 2.
Summary of ten fast-track SNPs analyzed in discovery and replication studies
| Discovery | Texas replication | UK replication | Combined | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ref. allelea | Chromosome | Position (bp) | Nearest gene or RNAb | OR (95% CI) |
P valuec (trend P) |
OR (95% CI) |
P valuec (trend P) |
OR (95% CI) |
P valuec (trend P) |
OR (95% CI) |
P value (ind.)d (P value (rep.)e) |
|
| rs2808630 | G | 1 | 156493941 | CRP | 0.76 | 2.05 × 10−5 | 0.93 | 0.426 | Not done | 0.82 | 7.40 × 10−6 | |
| (0.67–0.86) | (1.60 × 10−5) | (0.79–1.10) | (0.421) | (0.74–0.91) | (0.426) | |||||||
| rs7626795 | G | 3 | 191833163 | ILlRAP | 1.46 | 2.12 × 10−5 | 1.05 | 0.709 | 1.05 | 0.512 | 1.16 | 7.80 × 10−6 |
| (1.23–1.74) | (1.94 × 10−5) | (0.83–1.32) | (0.708) | (0.891–1.20) | (0.512) | (1.05–1.28) | (0.451) | |||||
| rs2202507 | C | 4 | 145615286 | GYPA | 1.30 | 8.49 × 10−6 | 0.92 | 0.267 | 1.00 | 0.970 | 1.06 | >1 × 10−5 |
| (1.16–1.46) | (8.67 × 10−6) | (0.79–1.06) | (0.262) | (0.91–1.09) | (0.970) | (1.00–1.14) | (0.556) | |||||
| rs11099666 | G | 4 | 148991033 | ARHGAP10 | 0.65 | 4.90 × 10−5 | 0.82 | 0.143 | 1.03 | 0.667 | 0.86 | >1 × 10−5 |
| (0.53–0.80) | (4.45 × 10−5) | (0.64–1.07) | (0.144) | (0.89–1.21) | (0.664) | (0.78–0.97) | (0.704) | |||||
| rs1481847f | A | 8 | 72944049 | MSC | 1.30 | 1.04 × 10−5 | 1.12 | 0.144 | 0.98 | 0.613 | 1.09 | 1.25 × 10−5 |
| (1.16–1.47) | (1.21 × 10−5) | (0.96–1.31) | (0.142) | (0.89–1.07) | (0.620) | (1.02–1.16) | (0.770) | |||||
| rs855974 | C | 10 | 119436858 | EMX2 | 0.74 | 1.42 × 10−5 | 1.02 | 0.849 | 1.00 | 0.948 | 0.92 | >1 × 10−5 |
| (0.65–0.85) | (1.37 × 10−5) | (0.85–1.21) | (0.848) | (0.91–1.11) | (0.948) | (0.85–0.99) | (0.880) | |||||
| rs8034191 | A | 15 | 76593078 | L0C123688 | 1.30 | 1.76 × 10−5 | 1.34 | 0.00036 | 1.33 | 1.94 × 10−11 | 1.32 | 3.15 × 10−18 |
| (1.15–1.47) | (1.94 × 10−5) | (1.14–1.57) | (0.00047) | (1.22–1.44) | (3.61 × 10−11) | (1.24–1.41) | (2.88 × 10−14) | |||||
| rs1051730 | G | 15 | 76681394 | CHRNA3 | 1.31 | 9.84 × 10−6 | 1.33 | 0.00042 | 1.32 | 2.33 × 10−10 | 1.32 | 7.00 ×10−18 |
| (1.16–1.48) | (1.14 × 10−5) | (1.13–1.55) | (0.00052) | (1.20–1.43) | (3.53 × 10−10) | (1.23–1.39) | (3.91 × 10−13) | |||||
| rs12956651 | G | 18 | 68265435 | CBLN2 | 0.59 | 1.09 × 10−5 | 0.84 | 0.232 | 1.04 | 0.633 | 0.85 | >1 × 10−5 |
| (0.47–0.75) | (1.12 × 10−5) | (0.62–1.12) | (0.226) | (0.88–1.23) | (0.636) | (0.76–0.96) | (0.859) | |||||
| rs6069045g | C | 20 | 52949270 | DOK5 | 0.75 | 6.24 × 10−6 | 0.91 | 0.243 | 1.05 | 0.266 | 0.93 | >1 × 10−5 |
| (0.66–0.85) | (8.60 × 10−6) | (0.77–1.07) | (0.240) | (0.96–1.16) | (0.264) | (0.87–0.99) | (0.704) | |||||
a
Allele nomenclature was set according to definitions for top SNPs provided for Illumina Hap300 v1.1 platform.
b
Nearest known transcribed sequence, as reported by Illumina.
c
Top line is P value from χ2 test for alleles, bottom line is P value from Armitage-Doll trend test.
d
P values from joint analysis of data from all stages. P values Indicated as > 1 × 10−5 are not accurately computed because the replication P values were much less significant than the discovery P values.
e
P values from replication data only.
f
SNP rs1481848 was genotyped for rs1481847 by Taqman.
g
Previous name for this SNP was rs7353629.