Datasets

GWAS meta-analysis summary statistics for download

By downloading the data you agree to use the data for scientific purposes only, and you do not attempt to re-identify individual participants included in the summary statistics. Furthermore, you are not allowed to redistribute the downloaded files or to upload them into a public repository. The download will be logged and may be analyzed for statistical purposes.

TraitMethodMByte
Goiter risk2-step imputed GWAS215
Goiter riskconventional meta-analysis185
Thyroid gland volume2-step imputed GWAS207
Thyroid gland volumeconventional meta-analysis145

Description of columns
MarkerName chr:position:type (GRCh build 37)
Allele1 coding allele
Allele2 noncoding allele
Freq1 the frequency of allele1
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
rsid the RS identifier of the variant (if available)
Nearest gene the name of the nearest gene

Description of this dataset
The dataset includes the genome-wide association analysis (GWAS) meta-analysis results for goiter risk (linear model) and log-transformed thyroid gland volume (logistic regression model). The results sets include all genetic variants with a minor allele frequency of at least 1%. Variants with an effective sample size below 75% of the total (maximum) sample size were excluded in meta-analysis GWAS result files.

Citation for this dataset:
Nasr MK, König E, Fuchsberger C, Ghasemi S, Völker U, Völzke H, Grabe HJ, Teumer A. Removing array-specific batch effects in GWAS mega-analyses by applying a two-step imputation workflow reveals new associations for thyroid volume and goiter. medRxiv 2024.11.21.24317711; doi: https://doi.org/10.1101/2024.11.21.24317711

TraitStratumMByte
TSHoverall180
FT4overall176
FT3overall175
TT3overall174
FT3/FT4 ratiooverall164
TT3/FT4 ratiooverall166
low TSHoverall185
high TSHoverall182
Colocalization mRNAcomplete results16
Finemapping plotsSuSiE plots92

Description of columns
MarkerName chr:position:type (GRCh build 37)
Allele1 coding allele
Allele2 noncoding allele
Freq1 the frequency of allele1
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
rsid the RS identifier of the variant (if available)

Description of this dataset
The dataset includes the genome-wide association analysis (GWAS) meta-analysis results for thyrotropin (TSH), free thyroxine (FT4), free T3 (FT3), total T3 (TT3), the FT3/FT4 ratio, the TT3/FT4 ratio, high TSH levels, and low TSH levels of a sex-combined dataset. The GWAS on TSH, FT4, FT3 and TT3 were calculated using a linear model after inverse-normal transformation of the thyroid hormone measurements (outcome). The ratios were log-transformed prior to the GWAS. The high/low TSH 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. The colocalization results are described in the README included in the zip file.

Citation for this dataset:
Sterenborg R, Steinbrenner I, Li Y, Bujnis MN, Naito T, Marouli E et al. Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications. Nat Commun. 2024 Jan 30;15(1):888. doi: 10.1038/s41467-024-44701-9

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