Table 3. Linear regression analysis between tSNPs and HapMap lymphoblastoid cell line expression levels of MAPKAPK2, IL-10, IL-20, FCAMR and C1orf116.

Gene	Significant tSNP	Location	Disease Associated allele*	Effect on Expression level		Linear regression p-value‡
MAPKAPK2 (NM_004759) †	rs4129024	Intron 1	G	Decreased	0.003
	rs4311892	3.94 kbdownstream	G	No effect	0.193
MAPKAPK2 (NM_032960) †	rs4129024	Intron 1	G	No effect	0.066
	rs4311892	3.94 kbdownstream	G	No effect	0.055
IL-10	rs1878672	Intron 3	G	Decreased	0.022
	rs1800896	−1082 bp	A	Decreased	0.011
IL-20	rs1400986	−468 bp	T	No effect	0.404
FCAMR	rs10863962	2.24 kbdownstream	T	Increased	0.009
	rs2353550	−3.34 kbupstream	G	Increased	0.005
	rs2842711	−15.19 kbupstream	T	No effect	0.655
C1orf116	rs2842721	3.66 kbdownstream	A	No effect	0.187
	rs12138969	705 bpdownstream	A	No effect	0.609

^*Allele with increased frequency in children with JIA compared with controls. This corresponds to the minor alleles for all except rs4129024 where the frequency of major allele G is higher in cases than controls.

^†Two transcript encoding two different isoforms have been found for this gene. They code for the same number of exons but differ at the 3′UTR region.

^‡The linear regression model was used to evaluate the association between log2-transformed expression values and genotypes of tSNPs. Associations reaching nominal significance (p<0.05) are shown in bold. One SNP reached the Bonferroni corrected threshold for 12 tests of 0.0042 = 0.05/12.