Table 1.
Replication of whole blood VNTRs in independent cohorts.
| Replication | ||||||||
|---|---|---|---|---|---|---|---|---|
| Locus | Length | RU Length | Effect Size | Gene | Annotation | Icelandic | Geuvadis | |
| 1 | chr1:21440112–21440147 | 35 | 6 | 0.43 | NBPF3 | UTR | Y | Y |
| 2 | chr2:24084339–24084414 | 75 | 25 | −0.12 | TP53I3 | UTR | Y | Y |
| 3 | chr2:25161573–25161616 | 43 | 9 | 0.22 | POMC | Coding | Y | Y |
| 4 | chr2:112542424–112542500 | 76 | 25 | −0.18 | POLR1B | Coding | Y | Y |
| 5 | chr3:56557249–56557289 | 40 | 20 | −0.12 | CCDC66 | Coding | Y | Y |
| 6 | chr6:13328502–13328532 | 30 | 6 | 0.12 | TBC1D7 | UTR | Y | Y |
| 7 | chr7:64337190–64337240 | 50 | 13 | 0.09 | ZNF736 | UTR | Y | Y |
| 8 | chr8:86508719–86508765 | 46 | 23 | 0.13 | RMDN1 | UTR | Y | Y |
| 9 | chr10:102869497–102869605 | 108 | 36 | 0.22 | AS3MT | Coding | Y | Y |
| 10 | chr21:46228815–46228863 | 48 | 9 | −0.03 | LSS | UTR | Y | Y |
| 11 | chr17:75589192–75589228 | 36 | 6 | −0.06 | MYO15B | Coding | Y | - |
| 12 | chr1:46609102–46609134 | 32 | 16 | 0.09 | MOB3C | UTR | Y | N |
| 13 | chr5:80654880–80654954 | 74 | 9 | 0.04 | MSH3 | Coding | Y | N |
| 14 | chr9:137063433–137063550 | 117 | 39 | −0.15 | SAPCD2 | UTR | Y | N |
| 15 | chr14:61762420–61762454 | 34 | 17 | 0.03 | SNAPC1 | UTR | Y | N |
| 16 | chr19:12577507–12577551 | 44 | 22 | −0.09 | ZNF490 | UTR | Y | N |
| 17 | chr21:41316673–41316756 | 83 | 13 | −0.19 | FAM3B | UTR | Y | N |
| 18 | chr22:37805258–37805313 | 55 | 6 | 0.11 | H1F0 | UTR | Y | N |
| 19 | chr1:202187007–202187042 | 35 | 7 | 0.06 | PTPRVP | UTR | N | Y |
| 20 | chr17:18208488–18208544 | 56 | 7 | −0.13 | ALKBH5 | UTR | N | Y |
| 21 | chr17:76564106–76564152 | 46 | 9 | 0.11 | SNHG16 | UTR | - | N |
| 22 | chr17:56978047–56978107 | 60 | 20 | 0.15 | SCPEP1 | UTR | N | N |
| 23 | chr6:30163542–30163579 | 37 | 12 | 0.14 | TRIM15 | UTR | - | - |
Each row describes an eVNTR in whole blood from GTEx project(n = 652 individuals) identified with false discovery rate (FDR) <0.05 based on 100 permutations. Replication of the signal in whole blood tissue of the Icelandic cohort of 903 samples and in lymphoblastoid cell-lines from the Geuvadis cohort (462 samples) with the same direction of effect and FDR <0.05. For the Icelandic cohort, only the VNTRs that showed significant associations in GTEx were tested using unmapped reads plus reads mapped to those specific loci. Hence, we used the conservative p value cutoff from the smaller GTEx cohort. Length (respectively, RU length) refers to the total (respectively, repeat-unit length) of the VNTR.