Table 1 Summary of i2QTL variants and eQTL results.

From: Properties of structural variants and short tandem repeats associated with gene expression and complex traits

Variant Class

No. Variants

No. Common Variants (tested)

Lead SV/STR-Only QTLs

Lead Joint QTLs

SNV

41,826,418

5,834,257

 

8,148

INDEL

7,040,457

1,520,762

 

2,685

Deletion (DEL)

16,238

3,073

661

51

Duplication (DUP)

2,693

391

55

9

Multiallelic CNV (mCNV)

1,703

947

294

111

Other SV (BND)

4,612

1,146

89

8

Inversion INV

210

84

11

0

Reference Mobile Element Insertions (rMEI)

2,343

1,448

243

3

ALU

7,880

1,932

294

9

LINE1

1,175

196

31

1

SVA

442

96

28

2

Short Tandem Repeats (STR)

588,189

33,608

5,260

170

Total SV

37,296

9,313

1,706

194

Total SV/STR

625,485

42,921

6,966

364

Total

49,492,360

7,397,940

6,966

11,197

  1. Numbers in each category refer to the number of non-redundant variants that were within 1 Mb of a gene and used in the eQTL analyses. Variants used for eQTL mapping had ≥ 5% minor allele frequency for SNVs and indels and ≥5% non-mode allele frequency for SVs and STRs. Lead SV/STR-Only QTLs column shows the number of lead variants in the eQTL analysis using only SVs and STRs while Lead Joint QTLs column shows the number of lead variants in the eQTL analysis using SNVs, indels, SVs, and STRS.
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