rs10496515

Homo sapiens
T>C
LOC105373576 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0089 (2664/29876,GnomAD)
C=0091 (2673/29112,TOPMED)
C=0104 (522/5008,1000G)
C=0084 (323/3854,ALSPAC)
C=0094 (348/3708,TWINSUK)
chr2:116313637 (GRCh38.p7) (2q14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.116313637T>C
GRCh37.p13 chr 2NC_000002.11:g.117071213T>C

Gene: LOC105373576, uncharacterized LOC105373576(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105373576 transcript variant X1XR_923239.2:n.N/AIntron Variant
LOC105373576 transcript variant X2XR_923240.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.899C=0.101
1000GenomesAmericanSub694T=0.900C=0.100
1000GenomesEast AsianSub1008T=0.922C=0.078
1000GenomesEuropeSub1006T=0.908C=0.092
1000GenomesGlobalStudy-wide5008T=0.896C=0.104
1000GenomesSouth AsianSub978T=0.850C=0.150
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.916C=0.084
The Genome Aggregation DatabaseAfricanSub8724T=0.905C=0.095
The Genome Aggregation DatabaseAmericanSub834T=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1606T=0.895C=0.105
The Genome Aggregation DatabaseEuropeSub18410T=0.915C=0.084
The Genome Aggregation DatabaseGlobalStudy-wide29876T=0.910C=0.089
The Genome Aggregation DatabaseOtherSub302T=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29112T=0.908C=0.091
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.906C=0.094
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs104965153.92E-05alcohol and nictotine co-dependence20158304

eQTL of rs10496515 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 rs10496515 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.