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

BMC Medical Genomics

Table 4 The most significant associations from trans-eQTL analysis at q = 0.05.

SNP Locus	dbSNP	Location (bp)	Position	SNP Gene Symbol	mRNA Locus	Entrez ID	mRNA Gene Symbol	q_eQTL
chrXp22.11	rs4828879	23770	upstream	PRDX4	chr11p15.5	7140	TNNT3	0.003
chr7q32.3	rs277491	0	intron	PLXNA4	chr3p26-p25	7862	BRPF1	0.003
chr4q32.3	rs10517754	0	intron	FSTL5	chr22q12.1	25770	C22orf31	0.005
chr7q34	rs2363830	0	intron	DENND2A	chr11q23-q24	56	ACRV1	0.016
chr3q22.1	rs938243	0	intron	CPNE4	chr16q23.3	93517	SDR42E1	0.018
chr2q13	rs10496425	0	intron	CCDC138	chr7q11.23	7461	CLIP2	0.019
chr2q13	rs7591305	0	intron	CCDC138	chr7q11.23	7461	CLIP2	0.019
chr10q21.1	rs10509024	0	intron	PCDH15	chrXp11.23	778	CACNA1F	0.029
chr3p24.3	rs964910	561192	upstream	SGOL1	chr1q44	114548	NLRP3	0.029
chr21q21.1	rs2826728	0	intron	NCAM2	chr11p15.5	7140	TNNT3	0.029
chr21q21.1	rs2155798	0	intron	NCAM2	chr11p15.5	7140	TNNT3	0.029
chr1q43	rs2790645	135107	upstream	CHRM3	chr5q31-q32	5521	PPP2R2B	0.029
chr11q14.1	rs62388	0	intron	DLG2	chr7q34	154790	CLEC2L	0.029
chr3q26.33	rs9290675	34917	upstream	ZNF639	chr15q21	6938	TCF12	0.049

'Position' indicates SNP genomic location; ' q _eQTL' indicates FDR-adjusted significance. Annotation is shown for SNPs in the first 5 columns, then for mRNA expression; e.g. for the first (non-header) row of this table, the mRNA expression levels for gene TNNT3 were significantly associated with genotype at rs4828879, which is 23,770 base pairs upstream of the PRDX4 locus.

ISSN: 1755-8794