rs1057239

Homo sapiens
G>A
KIAA0040 : 5 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0419 (12556/29910,GnomAD)
A=0394 (11493/29118,TOPMED)
A=0315 (1576/5008,1000G)
A=0464 (1789/3854,ALSPAC)
A=0478 (1773/3708,TWINSUK)
chr1:175161068 (GRCh38.p7) (1q25.1)
AD | ND
GWASdb2
5   publication(s)
See rs on genome
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.175161068G>A
GRCh37.p13 chr 1NC_000001.10:g.175130204G>A

Gene: KIAA0040, KIAA0040(minus strand)

Molecule type Change Amino acid[Codon] SO Term
KIAA0040 transcript variant 2NM_014656.2:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant 1NM_001162893.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant 3NM_001162894.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant 4NM_001162895.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant 6NM_001319231.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant 5NM_001319230.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant X1XM_017002909.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant X2XM_017002910.1:c.N/A5 Prime UTR Variant
KIAA0040 transcript variant X3XM_017002911.1:c.N/A5 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.625A=0.375
1000GenomesAmericanSub694G=0.680A=0.320
1000GenomesEast AsianSub1008G=0.856A=0.144
1000GenomesEuropeSub1006G=0.561A=0.439
1000GenomesGlobalStudy-wide5008G=0.685A=0.315
1000GenomesSouth AsianSub978G=0.720A=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.536A=0.464
The Genome Aggregation DatabaseAfricanSub8702G=0.602A=0.398
The Genome Aggregation DatabaseAmericanSub836G=0.710A=0.290
The Genome Aggregation DatabaseEast AsianSub1622G=0.871A=0.129
The Genome Aggregation DatabaseEuropeSub18448G=0.536A=0.464
The Genome Aggregation DatabaseGlobalStudy-wide29910G=0.580A=0.419
The Genome Aggregation DatabaseOtherSub302G=0.730A=0.270
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.605A=0.394
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.522A=0.478
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology
23365539Large scale association analysis for drug addiction: results from SNP to gene.Guo XScientificWorldJournal
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs10572390.0000012alcohol and nictotine co-dependence22488850
rs10572390.00000193alcohol dependence21703634
rs10572390.00000201alcohol dependence20202923
rs10572390.00031alcohol dependence21956439

eQTL of rs1057239 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs1057239 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr1175127262175127638E067-2566
chr1175127726175127793E067-2411
chr1175121212175121706E069-8498
chr1175138495175138718E0698291
chr1175117508175117593E070-12611
chr1175131566175131616E0701362
chr1175131702175131793E0701498
chr1175131845175132044E0701641
chr1175132208175132358E0702004
chr1175169465175169525E07139261
chr1175169774175170871E07139570
chr1175121212175121706E072-8498
chr1175173548175173704E07343344
chr1175173714175173889E07343510
chr1175115170175115364E081-14840
chr1175115429175115500E081-14704
chr1175115737175116333E081-13871
chr1175116438175116534E081-13670
chr1175116763175117071E081-13133
chr1175117325175117401E081-12803
chr1175117508175117593E081-12611
chr1175120951175121040E081-9164
chr1175121212175121706E081-8498
chr1175127262175127638E082-2566
chr1175127726175127793E082-2411
chr1175173548175173704E08243344
chr1175173714175173889E08243510








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1175160861175163201E06730657
chr1175160861175163201E06830657
chr1175160861175163201E06930657
chr1175160861175163201E07130657
chr1175160861175163201E07230657
chr1175160861175163201E07330657
chr1175160861175163201E07430657
chr1175160861175163201E08230657