Table 1.
SNPs with a genome-wide significant association in the discovery cohort (KA06) and replicated in the second cohort (KA09)
| UniProt ID (gene symbol) Peptide | SNP | Chr:position | Freq | KA06 beta* (SE)† | P value | KA09 beta* (SE)† | P value | Pooled P value‡ |
| HPT (HP) | ||||||||
| AVGDKLPECEAVCGKPK | rs217184§ | 16:72105965 | 0.18 | 0.56 (0.08) | 1.7 × 10−12 | 0.46 (0.11) | 1.5 × 10−5 | 8.0 × 10−17 |
| GDKLPECEAVCGKPK | rs77303550§ | 16:72079657 | 0.18 | 0.47 (0.077) | 1.6 × 10−9 | 0.39 (0.11) | 2.4 × 10−4 | 1.5 × 10−12 |
| TEGDGVYTLNDKK | rs77303550§ | 16:72079657 | 0.18 | 0.71 (0.08) | 8.7 × 10−19 | 0.68 (0.11) | 1.0 × 10−10 | 4.4 × 10−27 |
| TEGDGVYTLNNEK | rs217184§ | 16:72105965 | 0.18 | 0.86 (0.08) | 2.8 × 10−27 | 0.58 (0.13) | 3.7 × 10−6 | 2.9 × 10−31 |
| VDSGNDVTDIADDGCPKPPEIAHGYVEHSVR | rs77303550§ | 16:72079657 | 0.18 | 0.4 (0.078) | 2.7 × 10−7 | 0.39 (0.11) | 1.9 × 10−4 | 4.3 × 10−10 |
| A1AT (SERPINA1) | ||||||||
| DTEEEDFHVDQVTTVK¶ | rs1243165 | 14:94844305 | 0.21 | −0.9 (0.075) | 3.6 × 10−33 | −0.6 (0.089) | 1.5 × 10−11 | 3.9 × 10−41 |
| IVDLVKELDRDTVFALVNYIFFK | rs17090693 | 14:94841331 | 0.21 | −0.88 (0.069) | 5.9 × 10−37 | −0.81 (0.096) | 3.0 × 10−17 | 3.1 × 10−52 |
| TLNQPDSQLQLTTGNGLFLSEGLK|| | rs709932 | 14:94849201 | 0.13 | −0.48 (0.08) | 3.0 × 10−9 | −0.57 (0.15) | 1.7 × 10−4 | 2.9 × 10−12 |
| CO3 (C3) | ||||||||
| LLDGVQNPR** | rs2230203 | 19:6710782 | 0.10 | −0.85 (0.12) | 4.2 × 10−13 | −0.44 (0.12) | 1.7 × 10−4 | 1.9 × 10−14 |
| APOE (APOE) | ||||||||
| LGADMEDVCGR†† | rs429358 | 19:45411941 | 0.18 | −0.52 (0.083) | 6.3 × 10−10 | −0.34 (0.10) | 7.8 × 10−4 | 3.9 × 10−12 |
| FETUA (AHSG) | ||||||||
| HTFMGVVSLGSPSGEVSHPR‡‡ | rs2070635 | 3:186336176 | 0.48 | 0.53 (0.057) | 7.0 × 10−21 | 0.36 (0.081) | 9.9 × 10−6 | 1.7 × 10−24 |
Beta: The additive effect of the minor allele on the abundance level of the peptide.
SE: SE of the effect (beta).
Pooled: KA06 and KA09 analyzed together.
rs217184 and rs77303550 are in LD (R2 = 0.95).
DTEEEDFHVDQVTTVK is located at position 226–241 of the protein. Position 237 has a natural variant, coded by the SNP rs6647, which is in LD with rs1243165.
TLNQPDSQLQLTTGNGLFLSEGLK is located at position 126–149 of the protein. Position 125 has a natural variant, coded by our top SNP rs709932.
LLDGVQNPR is located at position 307–315 of the protein. Position 314 has a natural variant coded by the SNP rs1047286, which is in LD with our top SNP rs2230203.
LGADMEDVCGR is located at position 122–132 of the protein. Position 130 has a natural variant, coded by our top SNP rs429358.
HTFMGVVSLGSPSGEVSHPR is located at position 318–337 of the protein. Position 317 has a natural variant, coded by the SNP rs35457250, which is not in strong LD with our top SNP rs2070635. The P value for rs35457250 (P value = 5.1E-14 in the pooled analyses) is not as significant as our top SNP.