Table 3. Location and annotation of top GWAS hits.
| Protein | SNP | P-value | Effect, β (s.e.) | Effect allele (reference) | chr:position* | Gene | Type |
|---|---|---|---|---|---|---|---|
| IL-6RA | rs4129267 | 4.39 × 10−58 | 0.84 (0.052) | T (C) | 1:154426264 | IL6RA | Intronic |
| CXCL10 | rs11548618 | 6.78 × 10−37 | 1.80 (0.14) | A (G) | 4:76943947 | CXCL10 | Nonsynonymous |
| CCL24 | rs6946822 | 2.02 × 10−36 | −0.62 (0.049) | T (C) | 7:75479448 | CCL24 | Intergenic, 36 kb upstream |
| rs11465293†,‡ | 7.95 × 10−13 | −0.63 (0.088) | A (G) | 7:75442723 | CCL24 | Nonsynonymous | |
| MIC-A | rs3869132 | 5.33 × 10−16 | −0.73 (0.090) | A (G) | 6:31410948 | MIC-A | Intergenic, 28 kb downstream |
| rs2263316† | 1.02 × 10−08 | 0.48 (0.083) | G (A) | 6:31421297 | MIC-A | Intergenic, 38 kb downstream | |
| CD40-L | rs148594123 | 1.07 × 10−25 | −0.96 (0.091) | A (G) | X:135741443 | CD40LG | Nonsynonymous |
| CXCL5 | rs425535§ | 4.27 × 10−26 | −0.86 (0.081) | T (T) | 4:74863997 | CXCL5 | Synonymous |
| rs2472649|| | 3.57 × 10−21 | −0.70 (0.074) | A (A) | 4:74857708 | CXCL5 | Intergenic, 4 kb downstream | |
| rs2393967† | 4.54 × 10−08 | 0.30 (0.052) | C (A) | 10:65133156 | JMJD1C | Intronic | |
| hK11 | rs117268623 | 5.25 × 10−18 | −1.48 (0.17) | T (C) | 19:51527970 | KLK11 | Nonsynonymous |
| Ep-CAM | rs201314303§ | 6.74 × 10−16 | −2.48 (0.31) | G (C) | 2:47612302 | EPCAM | Intronic |
| rs56398830† | 1.26 × 10−15 | −0.94 (0.12) | A (G) | 13:103701690 | SLC10A2 | Nonsynonymous | |
| IL-17RB | rs6801605 | 1.75 × 10−18 | −0.56 (0.064) | A (G) | 3:53876218 | CHDH | Intronic |
| IL17RB | 4 kb upstream | ||||||
| IL-12 | rs10045431 | 8.99 × 10−17 | 0.47 (0.057) | A (A) | 5:158814533 | IL12B | Intergenic, 57 kb upstream |
| VEGF-D | rs188779336§ | 1.11 × 10−15 | −1.58 (0.20) | G (C) | X:15308292 | ASB11 | Intronic |
| rs146086561¶ | 1.81 × 10−15 | −1.57 (0.20) | T (C) | X:15365438 | FIGF | Nonsynonymous | |
| E-selectin | rs507666 | 5.01 × 10−16 | −0.55 (0.067) | A (G) | 9:136149399 | ABO | Intronic |
| MIA | rs2230694§ | 6.83 × 10−17 | 0.66 (0.079) | G (A) | 19:41263403 | SNRPA | Synonymous |
| rs2607426|| | 1.13 × 10−16 | 0.65 (0.079) | G (A) | 19:41274713 | MIA | Intergenic, 6k upstream | |
| rs2233154¶,§ | 1.13 × 10−16 | 0.65 (0.079) | T (C) | 19:41281346 | MIA | UTR5 | |
| rs2233159¶,§ | 1.07 × 10−16 | −0.65 (0.079) | C (C) | 19:41283365 | MIA | UTR3 | |
| CCL19 | rs7775228 | 2.63 × 10−13 | 0.51 (0.069) | C (T) | 6:32658079 | HLA-DQB1 | Intergenic, 24 kb upstream |
GWAS, genome-wide association study; SNP, single-nulecotide polymorphism.
P-values were calculated from 1df Wald statistics χ2-values.
*In hg19 coordinates.
†Independent genome-wide significant loci as per conditional analysis on top-snp, reported P-values after conditioning on the top-hit.
‡rs11465293 was not discovered in the unconditional discovery-replication analysis and was subsequently rerun in a conditional discovery-replication analysis resulting in the P-values 3.9 × 10−9 and 6.7 × 10−5 for the discovery and replication cohorts, respectively.
§Imputed.
||When the top SNP(s) was imputed, the top ranking genotyped SNP was also included in the table.
¶In perfect LD (R2=1) with top-snp in our cohort.