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Life Science Database Archive
D-HaploDB

LD_bin Data (Phase II)

Data detail

info Data name LD_bin Data (Phase II)
info DOI 
info Description of data contents 

Results of LD bin calculations for D2 (Phase II) data sets. Files are in GFF format, and contains two kinds of lines, that are distinguishable by column# 3.
- LD_BIN line: SNPs in LD bin. tagSNPs and best tagSNPs (*) are marked.
- LD_BIN_BOUNDARIES: Limit of LD bin
*SNP that shows the highest mean r2 among the SNPs in the bin

info Data file 
File name:
bin_2R80M5.gff.gz
File URL:
https://dbarchive.biosciencedbc.jp/data/dhaplodb/LATEST/bin_2R80M5.gff.gz
File size:
12.1MB
info Simple search URL 
info Data acquisition method 

Genotype Data (Phase II)

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 SNP 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. tagSNP is the SNP that shows r2 >0.8 for all other members of the bin. Best tagSNP is the SNP that shows the highest mean r2 for all other members of the bin.

info Number of data entries 

SNP: 541,686 entries
LD Bin: 254,762 entries

Column NumberDefinition in GFF formatDescription
#1 seqname Chromosome that the SNP resides (e.g. Chr1)
#2 source name of dataset (e.g. CHM_2R80M5Z)
#3 feature description of data. SNP information or LD bin boundary(e.g. LD_BIN, LD_BIN_BOUNDARIES)
#4 start Chromosomal position of SNP or start position of bin (NCBI Build 35)
#5 end Chromosomal position of SNP or end position of bin
#6 score LD_BIN line: 2 for Best tagSNP, and 1 for tagSNP, and 0 for other SNP.
LD_BIN_BOUNDARIES line: always "."
#7 strand always "+"
#8 frame always ","
#9 attributes

This column contains the following items.
- ld_bin: LD bin name
- RSID: RefSNP ID (rs number)
- tagging: flag that indicates tagSNP
- besttag: flag that indicates Best tagSNP
- SNPID: unique ID given by Affymetrix
(e.g. ld_bin 2R80M5Z_10_1 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)