Table 1

The list of sQTL signals linked to GWAS signals.

Gene

AS typea

Target exonb (hg19)

sQTL SNPc

SNP type

GWAS trait (SNP)

GWAS references


ACADM

SE

+chr1:76194085-76194173

rs7524467

< = 300 bp

Metabolic traits (rs211718)

[78]

DRAM2

SE

-chr1:111682122-111682288

rs3762374

5' SS

Liver enzyme levels (gamma-glutamyl transferase) (rs1335645)

[79]

SP140

SE

+chr2:231110577-231110655

rs28445040

Exon

Chronic lymphocytic leukemia (rs13397985)

[42]

Multiple sclerosis (rs10201872)

[43]

Crohn's disease (rs7423615)

[39]

CAST

SE

+chr5:96076448-96076487

rs7724759

5' SS

Alcohol dependence (rs13160562)

[38]

ERAP2

A5SSd

+chr5:96235824-96235949

rs2248374

5' SS

Crohn's disease (rs2549794)

[39]

Ankylosing spondylitis (rs30187)

[80]

MRPL11

A5SSd

-chr11:66206102-66206319

rs11110

Exon

Bipolar disorder (rs2242663)

[81]

ARL6IP4

A3SSe

+chr12:123466117-123466426

rs55742290

3' SS

Platelet counts (rs7296418, rs1727307)

[82]

ULK3

MXEf

-chr15:75130091-75130139

rs12898397

5' SS

Coffee consumption (rs6495122)

[83]

Coronary heart disease (rs2472299)

[84]

ATP5SL

SE

-chr19:41939176-41939339

rs1043413

Exon

Height (rs17318596)

[41]

ITPA

SE

+chr20:3193814-3193872

rs1127354

Exon

Response to hepatitis C treatment (rs11697186, rs6139030)

[50]

Ribavirin-induced anemia (rs1127354)

[85]


aAS type: SE, skipped exon; A5SS, alternative 5' splice site; A3SS, alternative 3' splice site; MXE, mutually exclusive exons.

bExon coordinates are in hg19 with the start position 0 based and the end position 1 based. The direction (+/-) of transcription is denoted before the coordinates.

cThe significant sQTL SNP (FDR≤0.1) closest to the target exon. SNP position and P value from GLiMMPS can be found in Additional file 2.

dAlternative 5' SS: ERAP2, chr5:96235893; MRPL11, chr11:66206180.

eAlternative 3' SS: ARL6IP4, chr12:123466141.

fMutually exclusive alternative exon: ULK3, chr15:75130492-75130533.

Zhao et al. Genome Biology 2013 14:R74   doi:10.1186/gb-2013-14-7-r74

Open Data