Table 1 Replication of whole blood VNTRs in independent cohorts.

From: Variable number tandem repeats mediate the expression of proximal genes

       

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

-

-

  1. 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.
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