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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.
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Dataset ID

NHA000084

Type of data
GWAS for smoking behaviour
Access criteria
Unrestricted-access
Total data volume
2.0 GB
File formats
  • HTML
  • ZIP
Research
hum0014
Date published
2019-03-26
Date modified
2019-03-26
Secondary ID
hum0014.v14.smok.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0014.v14.asi.v1.zipAge of smoking initiation482 MB
hum0014.v14.cpd.v1.zipCigarettes per day493 MB
hum0014.v14.ens.v1.zipSmoking initiation [Ever vs never smokers]496 MB
hum0014.v14.fcs.v1.zipSmoking cessation [Former vs current smokers]495 MB
hum0014_README_SMK_GWAS.htmlDictionary file25.3 KB

Analysis method

Genotyping by array

Materials and participants
165,436 individuals whose smoking status is available
Sample description
gDNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Reference genome
GRCh37
QC and filtering
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6
QC for reference panel:
After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded.
QC after imputation:
Variants with imputation quality of Rsq < 0.7 and MAF < 0.01 were excluded.
Imputation
minimac [imputation (1000 genomes Phase I v3)]
Analysis method
GenCall software (GenomeStudio)
Variant count
Autosomes: 5,961,480 SNVs
Male X chromosome (age started smoking): 163,412 SNVs
Female X chromosome (age started smoking): 146,130 SNVs
Male X chromosome (number of cigarettes smoked): 166,111 SNVs
Female X chromosome (number of cigarettes smoked): 146,114 SNVs
Male X chromosome (smoking history): 166,138 SNVs
Female X chromosome (smoking history): 146,146 SNVs
Male X chromosome (smoking cessation history): 166,142 SNVs
Female X chromosome (smoking cessation history): 146,118 SNVs
Data use policy
NBDC data sharing policy (JGAP000001)