rs2169520

Homo sapiens
T>C
LOC107986417 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0234 (7027/29928,GnomAD)
C=0283 (8264/29118,TOPMED)
C=0229 (1148/5008,1000G)
C=0217 (835/3854,ALSPAC)
C=0205 (760/3708,TWINSUK)
chr5:63302626 (GRCh38.p7) (5q12.1)
ND
GWASdb2
2   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.63302626T>C
GRCh37.p13 chr 5NC_000005.9:g.62598453T>C

Gene: LOC107986417, uncharacterized LOC107986417(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107986417 transcript variant X1XR_001742676.1:n.N/AIntron Variant
LOC107986417 transcript variant X2XR_001742677.1:n.N/AIntron Variant
LOC107986417 transcript variant X3XR_001742678.1:n.N/AIntron Variant
LOC107986417 transcript variant X4XR_001742679.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.553C=0.447
1000GenomesAmericanSub694T=0.780C=0.220
1000GenomesEast AsianSub1008T=0.883C=0.117
1000GenomesEuropeSub1006T=0.806C=0.194
1000GenomesGlobalStudy-wide5008T=0.771C=0.229
1000GenomesSouth AsianSub978T=0.910C=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.783C=0.217
The Genome Aggregation DatabaseAfricanSub8700T=0.615C=0.385
The Genome Aggregation DatabaseAmericanSub838T=0.810C=0.190
The Genome Aggregation DatabaseEast AsianSub1614T=0.860C=0.140
The Genome Aggregation DatabaseEuropeSub18474T=0.826C=0.174
The Genome Aggregation DatabaseGlobalStudy-wide29928T=0.765C=0.234
The Genome Aggregation DatabaseOtherSub302T=0.750C=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.716C=0.283
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.795C=0.205
PMID Title Author Journal
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology
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
rs21695203E-07alcohol and nictotine co-dependence22488850

eQTL of rs2169520 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 rs2169520 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.