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Table 2 Top ranking SNPs identified from pooled genome wide association study and validation genotyping in the discovery cohort

From: Pooled genome wide association detects association upstream of FCRL3 with Graves’ disease

    GWAS pooled genotyping (Cases = 412, Controls = 498) Validation individual genotyping (Cases = 412, Controls = 480)
SNP name Location chr and bp Gene A1 P value OR_A1 F_A F_U P value* OR_A1*
(95 % CI)
Rs9676286 Chr19q13.43
58126481
ZNF134 intron A 1.08 × 10−8 2.08 0.047 0.023 5.54 × 10−3 2.28 (1.27, 4.09)
rs9644119 Chr8p21.2
26517817
DPYSL2
2124 bp downstream
T 9.10 × 10-8 1.78 0.177 0.128 0.033 1.36 (1.03, 1.79)
rs11722643 Chr4p16.1
10127484
Intergenic
WDR1 upstream, ZNF518B downstream
T 1.03 × 10−7 1.88 0.101 0.054 1.38 × 10−3 1.91 (1.28, 2.83)
Rs686806 Chr 11q22.3
107228533
CWF19L2 intron T 2.36 × 10−7 1.70 0.242 0.168 9.6 × 10−4 1.53 (1.19, 1.97)
rs62469516 Chr7q21.13
88958624
ZNF804B intron A 2.68 × 10−7 0.51 0.043 0.088 5.73 × 10−5 0.41 (0.26, 0.63)
rs73452600 Chr 7q34
142828104
PIP 1070 bp upstream A 3.49 × 10−7 1.90 0.099 0.061 3.37 × 10−3 1.80 (1.22, 2.67)
Rs1662312 Chr 18p11.31
3220450
MYOM1 upstream A 5.72 × 10−7 0.51 0.040 0.080 5.33 × 10−4 0.45 (0.29, 0.71)
rs1469893 Chr 15q14
34988664
GJD2
56015 bp
Downstream
A 6.58 × 10−7 0.58 0.05 0.104 6.86 × 10−5 0.44 (0.29, 0.66)
Rs17676303 Chr 1q23.1
157679691
FCRL3
9044 bp upstream
T 8.05 × 10−7 1.68 0.254 0.150 1.14 × 10−8 2.05 (1.57, 2.67)
rs28578508 Chr18q12.1
32316007
DTNA intron A 8.16 × 10−7 0.56 0.062 0.099 2.80 × 10−3 0.56 (0.39, 0.82)
rs78542322 Chr 6q14.1
77291670
Intergenic
IMPG1 upstream
HTR1B downstream
T 9.82 × 10−7 0.52 0.071 0.141 3.27 × 10−5 0.47 (0.33, 0.67)
Rs3818779 Chr 10q26.11
121140671
GRK5 intron A 1.51 × −6 1.94 0.059 0.029 2.08 × 10−3 2.30 (1.35, 3.9)
rs2141440 Chr 11q14.3
90898463
Intergenic MIR4490 and FAT3 A 4.48 × 10−6 0.58 0.078 0.097 0.34 0.84 (0.59, 1.20)
  1. F_U is individual genotyping minor allele frequency A1 in normal control, F_A is the allele frequency in Graves’ disease
  2. OR is odd ratio for having minor allele in Graves’ cases compared to normal controls
  3. *P values and odds ratios in validation genotyping were adjusted for age and sex