A case-control association study genotyped on the Immunochip using a total of 2,747 individuals affected with an Autoimmune Thyroid Disease (2,285 Graves' disease patients and 462 Hashimoto's thyroiditis patients) and 9,364 controls.  After SNP quality control a total of 103,875 SNPs were available for analysis.  The analysis was able to confirm 5 of the previously reported ATD loci at a permutation test derived significance threshold of p < 1.12 x 10-6, and identified 5 new loci, taking the total of significant loci to 10 in European individuals.

Study Type
Case-Control Study
Exclusion Criteria

Samples were excluded due to :-

  • Low call rate.
  • Non-European ancestry
  • Duplication and closely related sample pairs
  • Study participant relatedness, estimated by 'identity by state' (IBS) statistic

Markers were excluded due to :-

  • MAF in controls < 0.05
  • Low call rate in cases or controls (<95%).
  • Deviation from Hardy-Weinberg equilibrium in controls (HWE z-score > 5)
  • Located within the defined HLA region (NCBI build 36 - chr6:29690000-33498585)

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113296527-114009223PTPN22  rs2476601G > A0.0969.69e-23D1.63 (1.49-1.78)D
1p36.32chr1:2431888-2879054MMEL1  rs2843403C > T0.3625.63e-06D1.16 (1.09-1.23)D
1q23.1chr1:157510927-157848760FCRL3  rs7522061T > C0.4802.36e-05D4.47 (10.70-1.21)D
2p24.3chr2:12470974-12540990TRIB2  rs1534422A > G0.4551.76e-07D1.17 (1.11-1.25)D
2q33.2chr2:203768727-203951852ICOS  CTLA4  rs11571297G > A0.4932.09e-23D1.37 (12.5-1.45)D
3q28chr3:188351572-188422865LPP  rs13093110C > T0.4523.69e-08D1.19 (1.12-1.26)D
6q15chr6:90097116-90319078BACH2  rs72928038G > A0.1771.23e-07D1.23 (1.14-1.32)D
6q27chr6:166932015-167134466RP11-517H2.6  CCR6  FGFR1OP  rs368397331A > C0.4081.64e-07D1.18 (1.11-1.25)D
10p15.1chr10:5988280-6129961IL2RA  rs706779A > G0.4672.67e-07D1.18 (1.1-1.25)D
11q21chr11:95537638-95599614rs4409785T > C0.1737.69e-08D1.23 (1.14-1.33)D
12q12chr12:41954222-42498232PRICKLE1  rs4768412C > T0.3633.56e-06D1.16 (1.09-1.23)D
14q31.1chr14:80636325-81113845TSHR  rs2300519T > A0.3801.34e-38D1.54 (1.44-1.64)D
16p11.2chr16:30644231-31371983ITGAM  rs57348955G > A0.3965.13e-08D1.19 (1.12-1.27)D


GDXHsS00018 meets the following criteria:

Criteria Name
Disease Tags
Study for a Disease 


PMIDTitleFirst AuthorJournalDisease(s)Date