Complex nature of SNP genotype effects on gene expression in primary human leucocytes

Heap, Graham A; Trynka, Gosia; Jansen, Ritsert C; Bruinenberg, Marcel; Swertz, Morris A; Dinesen, Lotte C; Hunt, Karen A; Wijmenga, Cisca; vanHeel, David A; Franke, Lude

doi:10.1186/1755-8794-2-1

BMC Medical Genomics

Table 2 Genes containing multiple probes that are affected by SNPs that also affect other probes in the same gene, but with opposite allelic directions

From: Complex nature of SNP genotype effects on gene expression in primary human leucocytes

Source	SNP	HUGO	Spearman	Probe	Unique Illumina Identifier*	Probe Sequence	Number of dbSNP polymorphisms known within probe region
Celiac	rs1131383	POLR2J	-0.48	GI_62422568	ILMN_1657317		0
HapMap	rs1131383	POLR2J	0.57	GI_21704275	4210731		0
Celiac	rs1901198	IRF5	-0.6	GI_38683857	ILMN_1670576		0
HapMap	rs1901198	IRF5	0.5	GI_38683858	1770358		0
Celiac	rs6565724	LOC400566	0.67	GI_62177143	ILMN_1713803		0
HapMap	rs6565724	LOC400566	-0.72	GI_37544593	6040008		0
HapMap	rs6565724	LOC400566	-0.74	GI_42661283	103170403		0
Celiac	rs2863095	MRPL43	0.45	GI_28872731	ILMN_1652147		0
Celiac	rs2863095	MRPL43	-0.49	GI_28872733	ILMN_1700477		0
HapMap	rs2863095	MRPL43	0.58	GI_28872731	3940465		0
HapMap	rs2863095	MRPL43	-0.61	GI_28872733	5900487		0
HapMap	rs4768933	DIP2B	0.42	GI_17457388	101780735		0
HapMap	rs4768933	DIP2B	-0.44	GI_39930390	3940278		0
Celiac	rs10774679	OAS1	-0.54	GI_74229010	ILMN_1658247		0
Celiac	rs10774679	OAS1	0.51	GI_74229012	ILMN_1672606		0
HapMap	rs3177979	OAS1	0.63	GI_8051620	2100154		0
HapMap	rs3177979	OAS1	-0.72	GI_8051622	2100048		0
Celiac	rs1040404	TIPRL	-0.47	GI_73088904	ILMN_1779432		0
Celiac	rs1040404	TIPRL	0.5	GI_73088933	ILMN_1781457		0
HapMap	rs222851	C17orf81	-0.72	GI_44662825	6380129		0
HapMap	rs222851	C17orf81	0.64	GI_44662829	2760301		0
Celiac	rs34374	PAM	0.43	GI_21070979	ILMN_1788631	GGCTACAGTCGAAAAGGGTTTGACCGGCTTAGCACTGAGGGCAGTGACCA	0
HapMap	rs34374	PAM	-0.41	GI_21070979	60056	GCCAGTGTCTTTCTTTGGTGCCTTTCCTGTTCAGCATTCTTAGCCTGTGG	0
HapMap	rs2838859	POFUT2	-0.48	GI_34147486	5900341		1
HapMap	rs2838859	POFUT2	0.45	Hs.300736	106110059		0
Celiac	rs7084722	PTER	-0.43	GI_47933342	ILMN_1795336		0
HapMap	rs7084722	PTER	0.48	GI_20070185	5570040		1
Celiac	rs10503170	MYOM2	0.43	GI_4505314	ILMN_1716733	ATTTTCACGGGTGTGGGCACATGGGTGTGGCACCTGGACGTGTGCAGCAT	1
HapMap	rs10503170	MYOM2	-0.42	GI_4505314	6620154	TTTACACGAGGGTAGACGGCAGATGCCTGACAGAGAGTGGGTTGGCAGAC	1
Celiac	rs11680305	ADI1	-0.42	GI_8922761	ILMN_1795671	CCGGTGGTGTGATGATGCCATATACCGCAGGGCTTGCTTCTGTCAAGTGT	1
HapMap	rs11680305	ADI1	0.41	GI_8922761	4730070	GAGCTCCCACCCTAAGGGGCACACACTGAGTTGCTTATGCCACTTCCTTG	0
Celiac	rs2395185	HLA-DRB5	-0.41	GI_26665892	ILMN_1697499	GGCTCTTATTCTTCCACAAGAGAGGACTTTCTCAGGCCCTGGTTGCTACC	3
HapMap	rs2395185	HLA-DRB5	0.47	GI_26665892	450332	ACGGCCTCCCATGCATCTGTACTCCCCCTGTGTGCCACAAATGCACTACG	8

Meta-analysis of different significant but opposite allelic effects of SNPs (FDR = 0.05, SNP-probe midpoint distance < 250 kb) in the celiac peripheral blood dataset and HapMap B cell line data set. Shown are 14 genes that contain probes for either of the two platforms but that show opposite allelic directions. If probes have identical identifiers on the two platforms, but different oligonucleotide sequences, the oligonucleotide sequences are indicated.
*As provided by Illumina platform record.

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ISSN: 1755-8794

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