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Life Science Database Archive
D-HaploDB

LD bin list (Phase II)

Data detail

info Data name LD bin list (Phase II)
info DOI 
info Description of data contents 

LD bin list of D2 (Phase II). LD bin is a group of SNPs that mutually shows high LD (r2 > 0.8). See below for detail.

info Data file 
File name:
dhaplo_d2_ld_bin_list.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/dhaplodb/LATEST/dhaplo_d2_ld_bin_list.zip
File size:
3.0MB
info Simple search URL 
info Data acquisition method 

Perlegen 281K arrays、Affymetrix 500K arrays

info Data analysis method 

Common SNPs (MAF > 5%) were selected, and LDs (r2 values) between every SNP pairs within 300 kb were calculated. LD bins were collected so that every pairs within the bin shows r2 >0.8, by the greedy method of ldSELECT (Carson et al., AJHG 74, 106-120, 2004) after the program was modified so that it can handle haploid data.

info Number of data entries 

254,762 entries

Data itemDescription
LD bin Name of LD bin
Chromosome Chromosome number each LD bin resides (Chr1 - Chr22, ChrX)
Position Start Start position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35)
Position End End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35)
SNPs Count Number of SNPs in LD bin
tagSNPs Count Number of tagSNPs in LD bin
Best tagSNP tagSNP that showed the highest mean r2, given by RefSNP ID (rs number)