rs4650716

Homo sapiens
C>A
KIAA0040 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0445 (13315/29898,GnomAD)
C==0425 (12389/29118,TOPMED)
C==0333 (1666/5008,1000G)
A=0492 (1898/3854,ALSPAC)
A=0487 (1806/3708,TWINSUK)
chr1:175159575 (GRCh38.p7) (1q25.1)
AD
GWASdb2
2   publication(s)
See rs on genome
27 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.175159575C>A
GRCh37.p13 chr 1NC_000001.10:g.175128711C>A

Gene: KIAA0040, KIAA0040(minus strand)

Molecule type Change Amino acid[Codon] SO Term
KIAA0040 transcript variant 2NM_014656.2:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant 1NM_001162893.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant 3NM_001162894.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant 4NM_001162895.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant 6NM_001319231.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant 5NM_001319230.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant X1XM_017002909.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant X2XM_017002910.1:c.N/A3 Prime UTR Variant
KIAA0040 transcript variant X3XM_017002911.1:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.384A=0.616
1000GenomesAmericanSub694C=0.350A=0.650
1000GenomesEast AsianSub1008C=0.148A=0.852
1000GenomesEuropeSub1006C=0.478A=0.522
1000GenomesGlobalStudy-wide5008C=0.333A=0.667
1000GenomesSouth AsianSub978C=0.290A=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.508A=0.492
The Genome Aggregation DatabaseAfricanSub8706C=0.416A=0.584
The Genome Aggregation DatabaseAmericanSub836C=0.320A=0.680
The Genome Aggregation DatabaseEast AsianSub1616C=0.136A=0.864
The Genome Aggregation DatabaseEuropeSub18438C=0.494A=0.505
The Genome Aggregation DatabaseGlobalStudy-wide29898C=0.445A=0.554
The Genome Aggregation DatabaseOtherSub302C=0.300A=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.425A=0.574
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.513A=0.487
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

P-Value

SNP ID p-value Traits Study
rs46507162.57E-05alcohol dependence21703634

eQTL of rs4650716 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 rs4650716 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 )
chr1175127262175127638E067-1073
chr1175127726175127793E067-918
chr1175121212175121706E069-7005
chr1175138495175138718E0699784
chr1175117508175117593E070-11118
chr1175131566175131616E0702855
chr1175131702175131793E0702991
chr1175131845175132044E0703134
chr1175132208175132358E0703497
chr1175169465175169525E07140754
chr1175169774175170871E07141063
chr1175121212175121706E072-7005
chr1175173548175173704E07344837
chr1175173714175173889E07345003
chr1175115170175115364E081-13347
chr1175115429175115500E081-13211
chr1175115737175116333E081-12378
chr1175116438175116534E081-12177
chr1175116763175117071E081-11640
chr1175117325175117401E081-11310
chr1175117508175117593E081-11118
chr1175120951175121040E081-7671
chr1175121212175121706E081-7005
chr1175127262175127638E082-1073
chr1175127726175127793E082-918
chr1175173548175173704E08244837
chr1175173714175173889E08245003








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1175160861175163201E06732150
chr1175160861175163201E06832150
chr1175160861175163201E06932150
chr1175160861175163201E07132150
chr1175160861175163201E07232150
chr1175160861175163201E07332150
chr1175160861175163201E07432150
chr1175160861175163201E08232150