PTS calculator for user-supplied SNP sets

  1. The Compute utility allows users to compute and visualize global PTS distributions for their own traits of interest.

  2. Users will need a collection of trait-associated SNPs, corresponding their trait of interest, in order to calculate and visualize PTS global distributions.

  3. Users should organize their trait-specific SNP sets in a tab delimited text file (the SNP table) with the following fields:
    1. SNP – the SNP rsID from dbSNP.
    2. Effect Allele – the specific allele {A, T, C, or G} that influences the expression of the trait of interest.
    3. Phenotype – a name or descriptor for the trait (phenotype) of interest. Note that users can include multiple traits for simultaneous PTS calculation from a single SNP table
    4. Effect size – the odds ratio (OR) or β-value that measures the magnitude of the effect for that SNP. If effect sizes are not available, users can leave this position empty, which will default to an unweighted PTS.

  4. An example SNP table is provided. The example table can be loaded to the server for a test computation, and/or it can be downloaded so that users can visually inspect the required format.

  5. Once the user SNP table is prepared:
    1. For users with < 1000 trait-associated SNPs:
      Paste or upload your SNP table in the form shown on the page To paste click on the upper left cell of the SNP table form and then paste.
    2. For users with >= 1000 trait-associated SNPs:
      Upload your SNP table and provide an email to get your results
Please note: The interactive calculator only accepts lists of 999 SNPs or fewer. Larger lists will be subset to the first 999 SNPs

SNP quality control

Users should pay close attention to quality control (QC) issues when assembling collections of trait-associated SNPs for PTS calculation. The PTS scores the GADGET computes are very much dependent upon the quality and accuracy of the input data. Specific QC issues that users may want to consider include, but may not be limited to:

  • correct (positive) SNP strand orientation
  • SNP strand ambiguity
  • low genotyping accuracy for indels
  • correct dbSNP build (150)
  • linkage disequilibrium (LD)

Choose a phenotype to explore

Distribution of PTS Worldwide


PTS Distribution by Population


PTS Distribution by Continental Group


Trait set information


Human population abbreviation key

1000 Genomes Global Population Groups

  • AFR - African

  • AMR - Admixed Americans

  • EAS - East Asian

  • EUR - European

  • SAS - Southeast Asian

1000 Genomes Population codes

Code Population Group
ACB African Caribbeans in Barbados AFR
ASW Americans of African Ancestry in SW USA AFR
ESN Esan in Nigeria AFR
GWD Gambian in Western Divisions in the Gambia AFR
LWK Luhya in Webuye Kenya AFR
MSL Mende in Sierra Leone AFR
YRI Yoruba in Ibadan Nigeria AFR
CLM Colombians from Medellin Colombia AMR
MXL Mexican Ancestry from Los Angeles USA AMR
PEL Peruvians from Lima Peru AMR
PUR Puerto Ricans from Puerto Rico AMR
CDX Chinese Dai in Xishuangbanna China EAS
CHB Han Chinese in Bejing China EAS
CHS Southern Han Chinese EAS
JPT Japanese in Tokyo Japan EAS
KHV Kinh in Ho Chi Minh City Vietnam EAS
CEU Utah Residents (CEPH) with Northern and Western European Ancestry EUR
FIN Finnish in Finland EUR
GBR British in England and Scotland EUR
IBS Iberian Population in Spain EUR
TSI Toscani in Italia EUR
BEB Bengali from Bangladesh SAS
GIH Gujarati Indian from Houston Texas SAS
ITU Indian Telugu from the UK SAS
PJL Punjabi from Lahore Pakistan SAS
STU Sri Lankan Tamil from the UK SAS

GADGET is intended as a tool for researchers to explore population-specific distributions of genetic variants that have been associated with a wide variety of human traits. Users of this site should treat the results with caution, as the interpretation PTS across populations can be complicated by a number of factors. We provide more detail on these issues on the Learn page and in our manuscript describing the server.

GADGET Compute Source Code: Github