Datasets

GWAS meta-analysis summary statistics for download


TraitStratumMByte
TSHoverall116
TSHwomen112
TSHmen119
FT4overall116
FT4women116
FT4men119
hyperthyroidism overall 123
hypothyroidism overall 124

Description of columns
MarkerName chr:position:type (GRCh build 37)
Allele1 coding allele
Allele2 noncoding allele
Freq1 the frequency of allele1 from the 1000Gv3 ALL ancestry reference panel
Effect the association effect of allele 1
StdErr the standard error of the effect
P.value the association p-value
N the total sample size
I2 the I2 heterogeneity measure

Description of this dataset
The dataset includes the genome-wide association analysis (GWAS) meta-analysis results of the discovery stage for thyrotropin (TSH), free thyroxine (FT4), increased TSH (hypothyroidism) and decreased TSH (hyperthyroidism) in the corresponding sex-strata. The GWAS on TSH and FT4 were calculated using a linear model after inverse-normal transformation of the thyroid hormone measurements (outcome). The hypo-/hyperthyroidism GWAS were calculated as a case-control analysis using a logistic regression model. The results sets include all genetic variants that passed final quality control filters, and that were included in the 1000Gv3 ALL ethnicities reference panel.
These summary statistics can also be obtained through the CHARGE dbGaP website (https://www.ncbi.nlm.nih.gov/gap) under accession number phs000930.

Citation for this dataset:
Teumer A, Chaker L, Groeneweg S, Li Y, Di Munno C, Barbieri C et al. Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation. Nat Commun. 2018;9: 4455. doi:10.1038/s41467-018-06356-1


TraitAnalysisMByte
TPOAb-positivitycase-control analysis52
TPOAb levelscontinuous trait50

Description of columns
SNPID rs number
chromosome chromosome
position position (NCBI build 36)
p_zscoreMeta p-value of the sample-size weighted meta-analysis (used as primary results in the publication)
Allele1 coding allele
Allele2 noncoding allele
Effect the association effect of allele 1
StdErr the standard error of the effect
P.value p-value of the inverse-variance weighted meta-analysis
I2 the I2 heterogeneity measure
N the total sample size

Description of this dataset
The dataset includes the genome-wide association analysis (GWAS) meta-analysis results of the discovery stage for Thyroid Peroxidase Antibodies (TPOAb).
The GWAS on continuous TPOAb levels were calculated using a linear model, the TPOAb-positivity as a case-control analysis using a logistic regression.
The z-score based p-values (p_zscoreMeta) were used as primary results in the publication because of the assay heterogeneity, where the remaining results were only calculated to get a rough estimation of the effect sizes.

Citation for this dataset:
Medici M, Porcu E, Pistis G, Teumer A, Brown SJ et al. Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease. PLoS Genet. 2014;10(2):e1004123. doi: 10.1371/journal.pgen.1004123