Table 3.

Potential causal exonic SNPs located by Immunochip dense genotyping. Conservation is by phastCons17way, study 99^th percentile = 0.998; 95^th percentile = 0.367. An essential splice site is a splice donor variant within the 2 base pair region at the 5′ end of an intron. A splice site is a sequence variant within 1-3 base pairs of the exon or 3-8 base pairs of the intron.

Chr	POS	Gene	SNP	MAF	r2 with lead	SNP Location	Allele	Amino acid change	Polyphen	SIFT	Conservation
1	2,535,613	MMEL1	rs4648562	0.33	1	Essential splice site	A	-	-	-	1
1	114,377,568	PTPN22	rs2476601	0.12	lead	Non-Synonymous coding	A	Arg620Trp	benign	tolerated	0.992
1	154,426,970	IL6R	rs2228145	0.38	lead	Non-Synonymous coding	C	Asp358Ala	benign	tolerated	0.008
3	58,183,636	DNASEIL3	rs35677470	0.09	lead	Non-Synonymous coding	A	Arg206Cys	probably damaging	deleterious	0.992
11	60,893,235	CD5	rs2229177	0.47	0.96	Non-Synonymous coding	C	Ala471Val	probably damaging	deleterious	0.835
19	10,449,358	ICAM3	rs7258015	0.23	1	Non-Synonymous coding/ Splice site	C	Arg115Gly	benign	tolerated	0
19	10,463,118	TYK2	rs34536443	0.04	lead	Non-Synonymous coding	G	Pro1104Ala	probably damaging	deleterious	0.189