NHGRI-EBI Catalog of Published Genome-Wide Association Studies (rs16867335)
  dbSNP: rs16867335
Position: chr2:181458934-181458934
Band: 2q31.3
Genomic Size: 1
View DNA for this feature (hg19/Human)
Reported region: 2q31.3
Publication: Xu W et al. A genome wide association study on Newfoundland colorectal cancer patients' survival outcomes. Biomark Res. 2015-03-19
Disease or trait: Survival in rectal cancer
Initial sample size: 171 European ancestry cases
Replication sample size: NA
Reported gene(s): intergenic
Strongest SNP-Risk allele: rs16867335-?
dbSNP build 144 observed alleles for rs16867335: C/T
Risk Allele Frequency: Not reported
p-Value: 4E-6 (overall survival)
Odds Ratio or beta: 3.27
95% confidence interval: [1.98-5.42]
Platform: Illumina [729737]
Copy Number Variant (CNV)?: No
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Data last updated: 2020-01-08

Description

This track displays single nucleotide polymorphisms (SNPs) identified by published Genome-Wide Association Studies (GWAS), collected in the NHGRI-EBI GWAS Catalog published jointly by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EMBL-EBI). Some abbreviations are used above.

From http://www.ebi.ac.uk/gwas/docs/about:

The Catalog is a quality controlled, manually curated, literature-derived collection of all published genome-wide association studies assaying at least 100,000 SNPs and all SNP-trait associations with p-values < 1.0 x 10-5 (Hindorff et al., 2009). For more details about the Catalog curation process and data extraction procedures, please refer to the Methods page.

Methods

From http://www.ebi.ac.uk/gwas/docs/methods:

The GWAS Catalog data is extracted from the literature. Extracted information includes publication information, study cohort information such as cohort size, country of recruitment and subject ethnicity, and SNP-disease association information including SNP identifier (i.e. RSID), p-value, gene and risk allele. Each study is also assigned a trait that best represents the phenotype under investigation. When multiple traits are analysed in the same study either multiple entries are created, or individual SNPs are annotated with their specific traits. Traits are used both to query and visualise the data in the Catalog's web form and diagram-based query interfaces.

Data extraction and curation for the GWAS Catalog is an expert activity; each step is performed by scientists supported by a web-based tracking and data entry system which allows multiple curators to search, annotate, verify and publish the Catalog data. Papers that qualify for inclusion in the Catalog are identified through weekly PubMed searches. They then undergo two levels of curation. First all data, including association information for SNPs, traits and general information about the study, are extracted by one curator. A second curator then performs an additional round of curation to double-check the accuracy and consistency of all the information. Finally, an automated pipeline performs validation of the extracted data, see the Quality control and SNP mapping section below for more details. This information is then used for queries and in the production of the diagram.

References

Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7. PMID: 19474294; PMC: PMC2687147