Table 2.
Functional annotation of the significant SNPs from 17 imputed regions.
| SNPs | Variant type | CADD score | Index SNPa | Relevant Geneb | Gene mapping |
|---|---|---|---|---|---|
| rs35760881 | Intergenic | 1.31 | rs35760881 | AKIP1 | Cis-eQTL |
| rs4362135 | Intergenic | 5.79 | |||
| rs6032870 | Intergenic | 2.30 | rs6032870 | TMX4 | Enhancer |
| rs2327290 | Intronic (SNAP25-AS1) | 0.29 | |||
| rs10211311 | Intronic (MTA3) | 1.34 | rs10211311 | MTA3 | Cis-eQTL; Positional |
| rs13011430 | Intronic (MTA3) | 0.03 | |||
| rs8179838 | Intronic (MTA3) | 7.22 | |||
| rs2135743 | Intronic (LINC01060) | 1.68 | rs2135743 | — | NA |
| rs10026052 | Intronic (LINC01060) | 4.52 | |||
| rs3818215 | Intronic (MYBL2) | 0.50 | rs3818215 | MYBL2 | Cis-eQTL; Positional |
| rs2070235 | Missense (MYBL2) | 17.80 | |||
| rs12208914 | Intronic (UST) | 0.09 | rs12208914 | UST | Positional |
| rs10983328 | Intronic (ASTN2) | 0.43 | rs10983328 | — | NA |
| rs4798499 | Intronic (ARHGAP28) | 7.05 | rs4798499 | ARHGAP28 | Positional |
| rs1379490 | Intronic (ZNF385D) | 1.27 | rs1379490 | KCNH8 | Enhancer |
| rs7629800 | Intronic (ZNF385D) | 9.47 | |||
| rs7645913 | Intronic (ZNF385D) | 3.78 | |||
| rs11743963 | Intergenic | 0.20 | rs11743963 | ZNF608 | Cis-eQTL |
| rs13180906 | Intergenic | 9.13 | |||
| rs2689089 | Intronic (ANKS1A) | 10.40 | rs2689089 | RPL10A | Cis-eQTL |
| rs11696299 | Intronic (TRIB3) | 5.08 | rs11696299 | RBCK1 | Cis-eQTL |
| rs1152954; | Intronic (MYRFL) | 15.55 | rs1152954 | CCT2 | Enhancer |
| rs710702 | Intronic (MYRFL) | 4.80 | |||
| rs9969211 | Intronic (DNAH11) | 2.17 | rs9969211 | CDCA7L | Cis-eQTL |
| rs10485983 | Intronic (DNAH11) | 6.35 | |||
| rs7670046 | Intronic (MAEA) | 2.11 | rs7670046 | SPON2 | Cis-eQTL |
| rs11727167 | Intronic (MAEA) | 2.70 | |||
| rs61045241 | Intergenic | 0.23 | rs61045241 | SDHAF3 | Enhancer |
| rs1799041 | Intergenic | 1.89 | |||
| rs9908136 | Intronic (PLXDC1) | 2.66 | rs9908136 | GSDMB | Cis-eQTL |
| rs16238 | Intronic (PLXDC1) | 2.67 |
Genotyped array SNPs are marked in bold. If the index SNP in the imputed region is the imputed one, then both imputed SNP and genotyped SNP of interest are mentioned otherwise, genotyped SNP of interests are mentioned only.
CADD: Combined Annotation Dependent Depletion
— No relevant genes.
NA: not applicable.
a
SNP with the lowest p-value in each of the 17 imputed regions.
b
Gene playing major role in pathways reported to be involved in spontaneous preterm birth.