[Credits]

Life Science Database Archive
D-HaploDB

LD_bin Data (Phase III)

Data detail

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

Results of LD bin calculations for D3 (Phase III) 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_3R80M5Zb36.gff.gz
File URL:
https://dbarchive.biosciencedbc.jp/data/dhaplodb/LATEST/bin_3R80M5Zb36.gff.gz
File size:
12.8MB
info Simple search URL 
info Data acquisition method 

Genotype Data (Phase III)

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 Tagzilla, which is based on the principle similar to ldSELECT (Carson et al., AJHG 74, 106-120, 2004). 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: 565,646 entries
LD Bin: 250,751 entries

Column NumberDefinition in GFF formatDescription
#1 seqname Chromosome that the SNP resides (e.g. Chr1)
#2 source name of dataset (e.g. CHM_3R80M5Z)
#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 36)
#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 3R80M5Z_10_2 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)