rs1954456

Homo sapiens
T>C / T>G
LOC644919 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0278 (8307/29796,GnomAD)
T==0245 (7144/29118,TOPMED)
T==0213 (1068/5008,1000G)
T==0276 (1064/3854,ALSPAC)
T==0279 (1036/3708,TWINSUK)
chr14:41086559 (GRCh38.p7) (14q21.1)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.41086559T>C
GRCh38.p7 chr 14NC_000014.9:g.41086559T>G
GRCh37.p13 chr 14NC_000014.8:g.41555764T>C
GRCh37.p13 chr 14NC_000014.8:g.41555764T>G

Gene: LOC644919, uncharacterized LOC644919(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02315 transcript variant 2NR_109758.1:n.N/AIntron Variant
LINC02315 transcript variant 1NR_109757.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.190C=0.810
1000GenomesAmericanSub694T=0.250C=0.750
1000GenomesEast AsianSub1008T=0.207C=0.793
1000GenomesEuropeSub1006T=0.259C=0.741
1000GenomesGlobalStudy-wide5008T=0.213C=0.787
1000GenomesSouth AsianSub978T=0.180C=0.820
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.276C=0.724
The Genome Aggregation DatabaseAfricanSub8702T=0.218C=0.782
The Genome Aggregation DatabaseAmericanSub834T=0.260C=0.74,
The Genome Aggregation DatabaseEast AsianSub1552T=0.157C=0.843
The Genome Aggregation DatabaseEuropeSub18406T=0.319C=0.680
The Genome Aggregation DatabaseGlobalStudy-wide29796T=0.278C=0.721
The Genome Aggregation DatabaseOtherSub302T=0.200C=0.80,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.245C=0.754
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.279C=0.721
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
rs19544565.73E-05alcohol and nictotine co-dependence20158304

eQTL of rs1954456 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 rs1954456 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.