Table 2 Numbers of markers identified as significantly associated with efficacy end points

(A) Overlap indicates the number of markers identified in more than one analysis. A marker is selected in White if P<10⁻⁵ in the White population. A marker is selected in All if P<10⁻⁴ in the White population and a lower P-value in the All population
End point	White	All	Overlap, White/All	White/All Overlap with LASSO of White	White/all Overlap with LASSO of All	Overlap LASSO White/LASSO All	Total
cDAS28	5	18	2	3	3	2	33
cSJC	4	25	1	0	2	2	44
cTJC	9	11	1	1	1^a	1	36
cHAQ	9	13	0	2	2	1	37
cCRP	14	15	0	0	0	2	45
ACR20	3	8	0	5	3	4	21

(B) SNP markers meeting genome-wide significance (P<10⁻⁷)
End point	Chr	SNP	Position	White, MAF	White HWE P	White β	White P	All P	Locus	Nearby genes (kb)
cSJC	2	rs11886534	3 815 178	0.44	0.54	−2.79	5.4e-08	1.4e-07	—	ALLC(−87)
cSJC	14	rs850246	56 430 538	0.30	0.63	2.99	7.9e-08	2.6e-06	—	OTX2(−88)
cCRP	9	rs13302591	132 054 458	0.16	0.53	0.57	8.2e-08	9.8e-06	—	FREQ(−25)
cCRP	6	rs12110787	161 394 956	0.10	0.58	0.54	3.0e-05	3.0e-08	MAP3K4	AGPAT4(82)

(C) Associations of SPTLC3 and MYOB18 sequencing-derived markers with cDAS28
Locus	Chr	SNP	Position	White MAF	White HWE P	White P	All P
SPTLC3	20	rs6105044	13 065 746	0.32	0.0047	2.3e-05	1.2e-06
SPTLC3	20	rs6041897	13 067 979	0.47	0.59	1.7e-05	3.5e-06
SPTLC3	20	rs6033625	13 073 273	0.32	0.13	1.3e-05	2.1e-06
SPTLC3	20	seq_rs67718002	13 085 393	0.13	0.45	1.3e-05	1.4e-06
MYOB18	22	rs6004918	24 784 171	0.18	0.20	1.2e-06	0.0007

Abbreviations: ACR, American College of Rheumatology; cCRP, change in C-reactive protein; cDAS28, change in Disease Activity Score; cHAQ, change in health assessment questionnaire score; cSJC, change in swollen joint count; cTJC, change in tender joint count; HWE, Hardy–Weinberg equilibrium; LASSO, least absolute shrinkage and selection operator; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.
^aOnly nine predictors selected in cTJC LASSO of All.
For details on individual markers see Supplementary Table 2.

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