GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data

Table 1 The list of sQTL signals linked to GWAS signals.

Gene	AS type^a	Target exon^b (hg19)	sQTL SNP^c	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	A5SS^d	+chr5:96235824-96235949	rs2248374	5' SS	Crohn's disease (rs2549794)	[39]
					Ankylosing spondylitis (rs30187)	[80]
MRPL11	A5SS^d	-chr11:66206102-66206319	rs11110	Exon	Bipolar disorder (rs2242663)	[81]
ARL6IP4	A3SS^e	+chr12:123466117-123466426	rs55742290	3' SS	Platelet counts (rs7296418, rs1727307)	[82]
ULK3	MXE^f	-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.

ISSN: 1474-760X