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.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)]. 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.
	Geography    Latitude    Absolute Latitude    Longitude Climate    Minimum Temperature (Winter)    Maximum Temperature (Summer)    Precipitation Rate (Summer)    Precipitation Rate (Winter)    Short Wave Radiation Flux (Summer)    Short Wave Radiation Flux (Winter)    Relative Humidity (Summer)    Relative Humidity (Winter) Ecoregion    Polar    Humid Temperate    Dry    Humid Tropical Subsistence/Main Dietary Component    Foraging    Horticulture    Pastoral    Intensive Agriculture    Cereals    Roots/Tubers    Fat/Meat/Milk All Variables
Maximum Transformed Rank	Environmental Variable
Filter results based on minimum level of LD with queried HapMap SNP.
	African Ancestry in USA (ASW; HapMap PhIII) CEPH Collection (CEU; HapMap PhI/II) Han Chinese in China (CHB; HapMap PhI/II) Chinese in USA (CHD; HapMap PhIII) Gujarati in USA (GIH; HapMap PhIII) Luhya in Kenya (LWK; HapMap PhIII) Mexican Ancestry in USA (MXL; HapMap PhIII) Maasai in Kenya (MKK; HapMap PhIII) Japanese in Tokyo (JPT; HapMap PhI/II) Toscani in Italia (TSI; HapMap PhIII) Yoruba in Nigeria (YRI; HapMap PhI/II)
Minimum r2	HapMap Population
global_61_pop
Analysis