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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000207

Type of data
allele counts and frequencies of 526,270 SNPs about general population living in Okinawa Prefecture
Access criteria
Unrestricted-access
Total data volume
28.7 MB
File formats
  • XLSX
  • ZIP
Research
hum0496
Date published
2026-02-27
Date modified
2026-02-27
Secondary ID
hum0496.v2.freq.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0496.v2.freq.v1.xlsxDictionary file10.0 KB
hum0496.v2.freq.v1.zip28.7 MB

Analysis method

Genotyping by array

Materials and participants
General Population living in Okinawa Prefecture n=10,135
Ryukyu Cluster (n = 8,715)
Hondo Cluster (n = 1,420)
  • Health status
    Healthy
  • Subject count
    10,135 (Individual)
  • Cohort
    Okinawa Biobank
  • Population
    Hondo, Ryukyu
Sample description
DNAs extracted from peripheral blood or saliva
  • Tissue
    Peripheral blood, Saliva
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
Reference genome
GRCh38
QC and filtering
QC1. Genotyping QC (Exclusion Criteria)
SNP call rate < 0.98
pHWE < 1×10−6
Sample call rate < 0.98
SNPs not included in the latest manifest file (ASA-24v1-0_E2.csv)
QC2. Blast QC
All Top Genomic Seq sequences listed in the Illumina Manifest file were blasted against the GRCh38 database, and non-single map SNPs were excluded.
QC3. Other Exclusion Criteria
(i) SNPs with ≥3 genotype mismatches, based on comparison with WGS (in-house) genotypes for 158 samples.
(ii) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Ryukyu cluster and in-house WGS data (n = 273).
(iii) SNPs with an allele frequency difference ≥ 0.05, based on comparison between the Hondo cluster and ToMMo 54k.
(iv) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Hondo cluster and 1KG30xJPT
Note 1) (iii) was applied to SNPs that were not assessed in (i) and (ii).
(iv) was applied to SNPs that were not assessed in (i), (ii), and (iii).
Note 2) SNPs not applied in (i) through (iv) due to absence of genotype data of in-house WGS data or allele frequency data in external database, are flagged as "NoCheck" in the table.
Analysis method
GenCall software (GenomeStudio)
Variant count
526,270 SNPs (When including the 22,635 SNPs marked "NoCheck" by the other exclusion criteria above, file name: OBi_FreqTable_20251226_QC_relaxed.tsv)
503,635 SNPs (When excluding the 22,635 SNPs marked "NoCheck" by the other exclusion criteria above, file name: OBi_FreqTable_20251226_QC_default.tsv)
Processed data type
Allele frequency
Data use policy
NBDC data sharing policy (JGAP000001)