dbCLINE



"Some special term seems desirable to direct attention to variation within groups, and I propose the word cline, meaning a gradation in measurable characters...Prefixes can be used to denote clines of different types, for example, genocline (gradient in genes), geocline (geographical cline), chronocline (paleontological trend), etc."
Julian Huxley, Clines: an Auxiliary Taxonomic Principle, Nature, 1938.

Description
Applying the method of Coop et al. (2010) [PubMed], the Di Rienzo lab conducted a genome-wide study to identify regions associated with variation in 20 environmental variables across 61 worldwide populations (52 HGDP + 4 HapMap Phase III + 5 in house genotyped on the Illumina 650Y platform; Hancock et al. 2010 [PubMed], 2011 [PubMed]). The complete results of this analysis can be accessed through this database portal.

The complete set of Bayes factors can be separately downloaded for the continuous (climate and geography) variables [climate.4.tar.gz (89 MB)] and categorical (ecoregion and subsistence) variables [ecoreg_subsist.tar.gz (90 MB)]. The population allele frequency data from which the Bayes factors were calculated is also available [freq_data.tar.gz (80 MB)].

Note: The transformed rank statistic has changed and is now calculated in the following manner: Each SNP's Bayes factor is calculated by averaging the results from 5 independent runs of Bayenv. The SNPs are binned as described previously (Hancock et al. 2011 [PubMed]). A standardized score is computed for each SNP using the mean and standard deviation of the Bayes factors in the SNP's bin. Finally, the SNP's empirical p-value is calculated based on the rank of its standardized score relative to the entire set of tested SNPs.

Instructions
Search using a RefSNP accession ID (rs number) for a HapMap SNP, a gene name (or Entrez Gene ID), or range of physical positions. If a search is performed on a HapMap SNP not genotyped on the 650Y platform, dbCLINE will retrieve those genotyped SNPs that are in high LD (r2 > 0.60) with the query SNP (see HapMap filter below).

Examples:
Single SNP: rs11868112
SNPs within 10 kb of SNP: rs11868112+10000
SNPs within gene: SLC24A5 or 283652
SNPs within 50 kb of gene: SLC24A5+50000 or 283652+50000
SNPs within range: Chr9:660,000..760,000 (assembly NCBI36/hg18)

Search
Landmark or Region:


Or upload a plain text file containing a list of SNPs (limit 500):
Filters:
Filter results based on variable of interest and empirical p-value threshold.
Maximum Transformed Rank Environmental Variable
  
Filter results based on minimum level of LD with queried HapMap SNP.
Minimum r2 HapMap Population
  
  
Analysis