Table 2.

Summary of variants in CXCR4 coding-region by deep resequencing

Chr	Pos	Ref	Obs	Exonic Function	ESP6500	1000G	dbSNP135	CASE Freq.	CTRL Freq.
chr2	136872553	G	A	synonymous SNV	0.000461	0.0014	rs144110709	0	1
chr2	136872565	G	C	synonymous SNV				0	1
chr2	136872705	T	C	nonsynonymous SNV				0	1
chr2	136872715	G	A	synonymous SNV	0.003306	0.0018	rs148279552	3	7
chr2	136872727	A	G	synonymous SNV	0.000077		rs146627075	1	0
chr2	136872970	G	T	nonsynonymous SNV				1	0
chr2	136873084	G	A	synonymous SNV	0.036983	0.06	rs2228014	40	41
chr2	136873341	T	G	nonsynonymous SNV	0.000308		rs56400844	2	0
chr2	136873491	G	C	nonsynonymous SNV				1	0
chr2	136873496	A	T	stopgain SNV				1	0

Chr chromosome, Pos position on human genome build hg19, Ref reference allele, Obs the variant allele observed in our JIA dataset, ESP6500 variant allele frequency in Exome Sequencing Project, 1000G variant allele frequency in Thousand Genome Project, dbSNP 135 SNP rs ID in Single Nucleotide Polymorphism database of human genome build 135, CASE Freq variant allele frequency among cases, CTRL freq variant allele frequency among controls