Gene-Expression-Guided Selection of Candidate Loci and Molecular Phenotype Analyses Enhance Genetic Discovery in Systemic Lupus Erythematosus

Table 2

Summary of the 4 SNPs associated with SLE phenotypes and the SCAN database results regarding ancestral background and representative associated transcripts.

SNP	Chr.	Nearby Gene	SLE association ancestry	Associated phenotype	SCAN ancestry	Representative SCAN transcripts
rs9521996 C	13	ANKRD10	AA	Anti-RNP	YRI	IRF3, MIF
rs1408806 G	9	TYRP1	EA	Anti-Sm	CEPH	CASP3, RIPK1
rs4894215 G	2	None within 200kb	EA	Anti-Ro	CEPH	HLADRB1, HLADQB1
rs9568401 G	13	DLEU2	EA, AA	IFN	YRI	IRAK2, NOD2

SNP: single nucleotide polymorphism, chr.: chromosome, SLE association ancestry: the ancestral background in which the SNP was associated with an SLE phenotype, SCAN ancestry: the ancestral background in which that SNP was associated with alternate gene expression, representative SCAN transcripts: genes which differentially expressed due to genotype at that SNP in the SCAN database; two transcripts of the >15 were chosen for inclusion in this table, with an emphasis on those transcripts with immune system relevance.