Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer

BMC Medical Genomics

Table 1 Two representative, significant creQTL associations.

creQTL 1
SNP Annotation
Locus	dbSNP	Location (bp)	Position	Gene Symbol	Gene Title
chr13q12.3-q13	rs9315220	304602	upstream	RFC3	replication factor C (activator 1) 3, 38 kDa
chr13q12-q13	rs9315220	227702	upstream	STARD13	StAR-related lipid transfer (START) domain containing 13
Gene Cluster Annotation
Locus	Entrez ID	q _creQTL	p _eQTL	Gene Symbol	Gene Title
chr1p31.1	10561	1.13 × 10^-4	0.21	IFI44	interferon-induced protein 44
chr1p31.1	10964		0.28	IFI44L	interferon-induced protein 44-like
chr10q23-q25	3433		0.21	IFIT2	interferon-induced protein with tetratricopeptide repeats 2
chr10q24	3437		0.49	IFIT3	interferon-induced protein with tetratricopeptide repeats 3
chr10q25-q26	3434		0.19	IFIT1	interferon-induced protein with tetratricopeptide repeats 1
chr12q24.1	4938		0.52	OAS1	2',5'-oligoadenylate synthetase 1, 40/46 kDa
chr21q22.3	4599		0.56	MX1	myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)
creQTL 2
SNP Annotation
Locus	dbSNP	Location (bp)	Position	Gene Symbol	Gene Title
chr1p31.1	rs2296697	0	intron	LPHN2	latrophilin 2
Gene Cluster Annotation
Locus	Entrez ID	q _creQTL	p _eQTL	Gene Symbol	Gene Title
chr2p25	6664	5.40 × 10^-4	0.92	SOX11	SRY (sex determining region Y)-box 11
chr3p14.3	57408		0.38	LRTM1	leucine-rich repeats and transmembrane domains 1
chr11q22.3	4317		0.10	MMP8	matrix metallopeptidase 8 (neutrophil collagenase)
chr14q11.2	9362		0.38	CPNE6	copine VI (neuronal)
chr21q22.3	54058		0.64	C21orf58	chromosome 21 open reading frame 58
NA	NA		0.35	NA	NA

For each of the two creQTLs shown in this table (labeled 'creQTL 1' and 'creQTL 2'), the associated SNP (labeled 'SNP Annotation') is first shown with annotation for the nearest coding genes in cis. Beneath the SNP annotation is annotation for the significantly associated, co-regulated gene cluster (labeled 'Gene Cluster Annotation'). These two significant associations correspond to the two loci shown in Figure 3. 'Position' indicates the relative location of the SNP relative to the nearest coding gene; 'Location (bp)' indicates the physical distance, in base pairs, between the SNP and the nearest coding genes; p _eQTL indicates unadjusted significance of standard eQTL analysis.

ISSN: 1755-8794