About This Database

LD bin list (Phase III)

Data description

Data name

DOI

10.18908/lsdba.nbdc00036-004

Description of data contents

LD bin list of D3 (Phase III). LD bin is a group of SNPs that mutually shows high LD (r<sup>2</sup> > 0.8). See below for detail.

Data file

File name :

dhaplo_d3_ld_bin_list.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/dhaplodb/LATEST/dhaplo_d3_ld_bin_list.zip

File size :

3.1MB

Simple search URL

http://togodb.biosciencedbc.jp/togodb/view/dhaplo_d3_ld_bin_list#en

Data acquisition method

Affymetrix SNP 6.0

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 tagzilla (which is a rapid method of bin selection based on the principle of ldSELECT (Carson et al., AJHG 74, 106-120, 2004)).

Number of data entries

250,751 entries

Data detail

Data item	Description
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 36)
Position End	End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 36)
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)(Link to dbSNP available in quick search)