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SNPTEST specifications


Unique identifier OMICS_04400
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.5.1
Stability Stable
Maintained Yes


No version available


  • person_outline Jonathan Marchini

Publication for SNPTEST

SNPTEST citations


Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
call_split See protocol

[…] The data were analyzed using sex-stratified logistic regression models in SNPTEST for all SNPs on autosomal chromosomes within 500 kb of previously identified risk loci, and/or those found to be nominally significant (p < 5 × 10−4) in a previous meta-analysis (Fig. ),. Sex- […]


Meta analysis of GWAS on both Chinese and European populations identifies GPR173 as a novel X chromosome susceptibility gene for SLE

PMCID: 5934841
PMID: 29724251
DOI: 10.1186/s13075-018-1590-3
call_split See protocol

[…] The X chromosomal SNPs passing quality control were analyzed for association using SNPTEST [], fitting a logistic regression model in males and females separately. The association for European data, which comprise samples derived from different cohorts [], was adjusted using four pr […]


Association of VAMP5 and MCC genetic polymorphisms with increased risk of Hirschsprung disease susceptibility in Southern Chinese children

PMCID: 5940112
PMID: 29695640
DOI: 10.18632/aging.101423

[…] Linkage disequilibrium (LD) patterns were analyzed and displayed by HaploView []. Logistic regression tests were performed using SNPTEST v2.5b []. Tests of independent contributions toward disease associations for SNPs in a single locus were done using logistic regression, adjusting for the effect of a specific SNP in the same […]


The genetics of smoking in individuals with chronic obstructive pulmonary disease

PMCID: 5892035
PMID: 29631575
DOI: 10.1186/s12931-018-0762-7
call_split See protocol

[…] formed into normally distributed Z scores using the R function ‘rntransform’ [] (Additional file : Figure S1). We performed GWAS for three transformed phenotypes: eCO, salivary cotinine and CPD using SNPTEST [] assuming an additive genetic model and adjusting for age, gender, and the first 5 genetic principal components (PCs). Since cotinine levels were measured in all subjects at baseline visit, […]


Genome wide association study identifies susceptibility loci for B cell childhood acute lymphoblastic leukemia

Nat Commun
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] utation in the German data set, eigenvectors were inferred using the “smartpca” component within EIGENSOFT v2.4 and adjustment was carried out by including the first two eigenvectors as covariates in SNPTEST during association analysis,. The inflation factor λ and λ1000 was again calculated for all SNPs post imputation, QC,. The association between each SNP and risk was calculated using SNPTEST as […]


Genome wide association study and meta analysis identify loci associated with ventricular and supraventricular ectopy

Sci Rep
PMCID: 5884864
PMID: 29618737
DOI: 10.1038/s41598-018-23843-z
call_split See protocol

[…] ng correlation structure to control for correlation of repeated measures (R geepack package). In studies with one ECG per participant (MESA, CHS), we estimated associations using logistic regression (SNPTEST, R geeglm package). Though multiple ECGs were available in MESA and CHS, only baseline visit data were used in accordance with analytic pipelines. In HCHS/SOL, we estimated associations among […]


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SNPTEST institution(s)
Department of Statistics, University of Oxford, Oxford, UK

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