Overview

A genome-wide association study meta-analysis of 735 individuals with systemic lupus erythematosus (cases) and 2,537 controls of European descent. Genotyping of the studies were performed on Illumina Infinium HumanHap300 beadchip. Data processing and quality control filtering were performed using custom R scripts. Imputation on regions containing significantly associated SNPs was performed, using the IMPUTE (v2.3.0) across HapMap and 1000 Genomes panels with correction for multiple testing calculated within region. In total 16 loci are described, three of which confirm previous associations.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoverySLENULL2537735--
Exclusion Criteria

Samples

  • Duplicates and cryptically related excluded.
  • PCA analysis to remove samples not representative of ancestral background.

 

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1q25.3chr1:184627672-184944870EDEM3  rs10911628C > A0.0732.30e-13D1.95 (1.77-2.16)D
2q14.3chr2:126993206-127016304BIN1  rs12993006C > T0.2104.00e-06D1.45 (1.35-1.56)D
2q24.1chr2:154793612-155715423KCNJ3  rs4544377A > G0.1202.00e-06D1.82 (0.48-0.62)D
2q32.3chr2:190995776-191143008STAT4  rs7574865G > T0.2305.10e-09D1.51 (1.41-1.62)D
3p26.3chr3:1556111-1647369CNTN6  rs4684256C > T0.2809.80e-08D1.48 (0.63-0.72)D
7p11.2chr7:54640268-54839028SEC61G  rs6946131T > C0.4701.80e-06D1.39 (1.3-1.47)D
7q32.1chr7:128911686-129137466IRF5  rs4728142G > A0.4607.10e-10D1.45 (1.37-1.55)D
7q32.1chr7:128911686-129137466TNPO3  rs10488631T > C0.1101.50e-13D1.83 (1.68-1.99)D
10q26.3chr10:133386787-133482510MTG1  rs10857712T > C0.2403.30e-06D1.52 (1.39-1.64)D
11p13chr11:34645356-35014482EHF  rs10466455T > C0.4201.90e-07D1.37 (1.3-1.47)D
15q14chr15:38253598-38524632FAM98B  rs11073328C > T0.0989.90e-15D1.94 (1.77-2.11)D
15q15.1chr15:41271772-41879602TYRO3  rs12259A > G0.0233.40e-06D10.0 (5.88-20.0)D
15q26.2chr15:97010453-97107241SPATA8  rs8023715C > A0.0751.20e-08D1.81 (1.64-2.00)D
16p11.2chr16:30879141-31373327ITGAM  rs9888739C > T0.1304.30e-11D1.64 (1.51-1.78)D
17q12chr17:39214888-40014592MED1  rs11655550T > C0.1606.70e-07D1.48 (1.37-1.59)D
20p13chr20:4726742-4803306RASSF2  rs6084875G > A0.3402.10e-06D1.36 (1.27-1.44)D
20q13.13chr20:49792078-50046045RNF114  rs11697848C > T0.0511.40e-11D2.12 (1.89-2.37)D

Criteria

GDXHsS00037 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date