. Author manuscript; available in PMC: 2017 Jan 1.

Published in final edited form as: Arthritis Rheumatol. 2016 Jan;68(1):174–183. doi: 10.1002/art.39403

Table 1.

New genome-wide significant SLE locus that was identified by Stage 1 and 2 analyses and then replicated in Stage 3 analysis

Chr	SNP	Position in bp (hg19)	Allele	Stage 1 discovery set 661 cases & 487 controls				Stage 2 data set 431 cases & 2,155 controls				Stages 1&2 Meta P	Stage 3 replication data set 4,036 cases & 6,959 controls					Nearest Protein- coding Gene^*	RegulomeDB score^**
Chr	SNP	Position in bp (hg19)	Allele	Case Freq	Contro l Freq	OR	P	Case Freq	Contro l Freq	OR	P	Stages 1&2 Meta P	Case Freq	Contro l Freq	OR	P	Impute d	Nearest Protein- coding Gene^*	RegulomeDB score^**
12q12	rs10506216	43130885	T	0.109	0.079	1.701	1.71E-03	0.124	0.080	1.666	5.04E-06	3.08E-08	0.093	0.081	1.167	2.27E-03	Yes	PRICKLE1	6
	rs1356422	43142996	G	0.239	0.184	1.570	2.02E-04	0.215	0.182	1.247	1.22E-02	3.46E-05	0.205	0.188	1.124	1.05E-03	Yes	PRICKLE1	5
	rs11181677	43150285	C	0.236	0.183	1.520	6.13E-04	0.209	0.181	1.204	4.00E-02	3.17E-04	0.205	0.189	1.121	1.40E-03	Yes	PRICKLE1	ND
	rs1914490	43214484	G	0.300	0.251	1.427	1.49E-03	0.268	0.238	1.186	3.47E-02	4.33E-04	0.270	0.257	1.072	3.29E-02	Yes	PRICKLE1	6

Only the SNPs with meta P<1.00E-03 and same direction of association in Stage 1 and 2 samples that had P<0.05 in Stage 3 sample are shown. Bold alleles: reverse strand alleles

The nearest protein-coding gene within ± 500 kb (http://www.genome.ucsc.edu/).

^**

Please see the methods section and http://www.regulomedb.org/help;

ND: No Data.; RegulomeDB scoring scheme is divided into the following categories (1 through 6) based on available data resources: "1a: expression Quantitative Trait Locus (eQTL) + Transcription factor (TF) binding + matched TF motif + matched DNase Footprint + DNase peak, 1b: eQTL + TF binding + any motif + DNase Footprint + DNase peak, 1c: eQTL + TF binding + matched TF motif + DNase peak, 1d: eQTL + TF binding + any motif + DNase peak, 1e: eQTL + TF binding + matched TF motif, 1f: eQTL + TF binding / DNase peak, 2a: TF binding + matched TF motif + matched DNase Footprint + DNase peak, 2b: TF binding + any motif + DNase Footprint + DNase peak, 2c: TF binding + matched TF motif + DNase peak, 3a: TF binding + any motif + DNase peak, 3b: TF binding + matched TF motif, 4: TF binding + DNase peak, 5: TF binding or DNase peak, 6: other".