Table 1. Most probable SNPs identified from computational fine mapping of regions associated with gestational duration.
Functional annotations are based on data from endometrial stromal cells. We list an annotation if the SNP is located in a sequence with that annotation in either untreated or decidualized condition. Functional prior is the prior probability of an SNP being a causal variant. For an SNP without any functional annotation, its prior probability is 3.6 × 10−6. We list the pcHi-C annotation if the SNP is within 1 kb of a region involved in a pcHi-C interaction. We call a gene the target of an SNP if (i) the SNP is located in the promoter (< 1 kb of transcription start site) of that gene or (ii) the promoter of that gene has a pcHi-C interaction with a region within 1 kb of the SNP. In the case of rs147843771 at the FOXL2 locus, the target was defined by literature evidence (69). The number of credible SNPs at each region is shown in Fig. 5B. SNPs in bold are discussed in the text. FOXL2 (69), forkhead box L2; GATA2, GATA-binding protein 2; HAND2, heart and neural crest derivatives expressed 2; KCNAB1, potassium voltage-gated channel subfamily A member regulatory beta subunit 1; WNT4, Wnt family member 4.
| SNP | Location (hg19) | GWAS P value | Functional prior | PIP |
Functional annotations |
Likely target |
| rs147843771 | chr3:138843356 | 3.8 × 10−8 | 8.3 × 10−5 | 0.74 | K4me1 | FOXL2 |
| rs17315501 | chr3:139029676 | 1.7 × 10−7 | 9.9 × 10−5 | 0.21 | K4me1, K4me3, ATAC, K27ac |
|
| rs2946164 | chr5:157884706 | 3.0 × 10−26 | 8.3 × 10−5 | 0.72 | K4me1 | |
| rs13141656 | chr4:174728703 | 3.9 × 10−7 | 5.1 × 10−4 | 0.38 | K4me1, K27ac, K4me3, ATAC, pcHi-C |
HAND2 (pcHi-C) |
| rs7663453 | chr4:174729014 | 4.5 × 10−7 | 5.1 × 10−4 | 0.33 | K4me1, K27ac, K4me3, pcHi-C |
HAND2 (pcHi-C) |
| rs13387174 | chr2:74206685 | 4.7 × 10−7 | 3.8 × 10−4 | 0.35 | pcHi-C, K4me1, K27ac | WBP1 (pcHi-C) |
| rs13390332 | chr2:74207357 | 2.0 × 10−7 | 9.9 × 10−5 | 0.18 | K4me1, K27ac | WBP1 (pcHi-C) |
| rs4677884 | chr3:123062970 | 4.1 × 10−9 | 8.3 × 10−5 | 0.34 | K4me1, ATAC | |
| rs56318008 | chr1:22470407 | 2.3 × 10−12 | 4.3 × 10−4 | 0.3 | K4me1, K4me3, ATAC, pcHi-C |
WNT4 (promoter) |
| rs55938609 | chr1:22470451 | 2.3 × 10−12 | 4.3 × 10−4 | 0.3 | K4me1, K4me3, ATAC, pcHi-C |
WNT4 (promoter) |
| rs3820282 | chr1:22468215 | 6.4 × 10−13 | 1.1 × 10−4 | 0.27 | K4me1, K4me3, ATAC |
WNT4 (promoter) |
| rs4679761 | chr3:155868039 | 5.0 × 10−9 | 9.9 × 10−5 | 0.24 | K4me1, K27ac | KCNAB1 (pcHi-C) |
| rs9882088 | chr3:155867092 | 5.5 × 10−9 | 8.3 × 10−5 | 0.19 | K4me1 | |
| rs3122173 | chr3:127889287 | 5.4 × 10−12 | 3.2 × 10−4 | 0.18 | K4me1, pcHi-C | GATA2 (pcHi-C) |
| rs2999048 | chr3:127878416 | 2.0 × 10−12 | 8.3 × 10−5 | 0.12 | K4me1, K27ac, pcHi-C |
GATA2 (pcHi-C) |
| rs1554535 | chr3:127895986 | 1.2 × 10−11 | 3.8 × 10−4 | 0.10 | K4me1, pcHi-C, K27ac |
GATA2 (pcHi-C) |