rs1554075

Homo sapiens
T>C
LOC729307 : Non Coding Transcript Variant
LOC105377441 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0347 (10409/29916,GnomAD)
T==0349 (10163/29118,TOPMED)
T==0330 (1653/5008,1000G)
T==0339 (1308/3854,ALSPAC)
T==0336 (1247/3708,TWINSUK)
chr4:137198353 (GRCh38.p7) (4q28.3)
AD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.137198353T>C
GRCh37.p13 chr 4NC_000004.11:g.138119507T>C

Gene: LOC729307, uncharacterized LOC729307(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02510 transcriptNR_134640.1:n.156...NR_134640.1:n.1562T>CT>CNon Coding Transcript Variant

Gene: LOC105377441, uncharacterized LOC105377441(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377441 transcript variant X1XR_001741835.1:n.N/AIntron Variant
LOC105377441 transcript variant X2XR_001741836.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.357C=0.643
1000GenomesAmericanSub694T=0.440C=0.560
1000GenomesEast AsianSub1008T=0.150C=0.850
1000GenomesEuropeSub1006T=0.341C=0.659
1000GenomesGlobalStudy-wide5008T=0.330C=0.670
1000GenomesSouth AsianSub978T=0.390C=0.610
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.339C=0.661
The Genome Aggregation DatabaseAfricanSub8706T=0.365C=0.635
The Genome Aggregation DatabaseAmericanSub836T=0.410C=0.590
The Genome Aggregation DatabaseEast AsianSub1606T=0.143C=0.857
The Genome Aggregation DatabaseEuropeSub18466T=0.354C=0.645
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.347C=0.652
The Genome Aggregation DatabaseOtherSub302T=0.370C=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.349C=0.651
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.336C=0.664
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs15540754.76E-05alcohol consumption23743675

eQTL of rs1554075 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 rs1554075 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 )
chr4138127852138128346E0708345
chr4138127852138128346E0748345
chr4138134603138134662E07415096
chr4138134825138135023E07415318
chr4138127852138128346E0818345
chr4138127852138128346E0828345