rs7540557

Homo sapiens
T>C
LOC107984931 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0293 (8776/29910,GnomAD)
C=0318 (9285/29118,TOPMED)
C=0409 (2047/5008,1000G)
C=0211 (812/3854,ALSPAC)
C=0198 (733/3708,TWINSUK)
chr1:24051454 (GRCh38.p7) (1p36.11)
AD
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.24051454T>C
GRCh37.p13 chr 1NC_000001.10:g.24377944T>C

Gene: LOC107984931, uncharacterized LOC107984931(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107984931 transcriptXR_001737929.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.548C=0.452
1000GenomesAmericanSub694T=0.790C=0.210
1000GenomesEast AsianSub1008T=0.415C=0.585
1000GenomesEuropeSub1006T=0.770C=0.230
1000GenomesGlobalStudy-wide5008T=0.591C=0.409
1000GenomesSouth AsianSub978T=0.510C=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.789C=0.211
The Genome Aggregation DatabaseAfricanSub8694T=0.583C=0.417
The Genome Aggregation DatabaseAmericanSub834T=0.730C=0.270
The Genome Aggregation DatabaseEast AsianSub1614T=0.408C=0.592
The Genome Aggregation DatabaseEuropeSub18466T=0.790C=0.210
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.706C=0.293
The Genome Aggregation DatabaseOtherSub302T=0.690C=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.681C=0.318
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.802C=0.198
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs75405570.00025alcohol dependence(early age of onset)20201924
rs75405570.00059alcohol dependence20201924

eQTL of rs7540557 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:24377944PNRC2ENSG00000189266.7T>C1.5432e-2092345Cerebellum
Chr1:24377944PNRC2ENSG00000189266.7T>C1.0478e-2492345Cortex
Chr1:24377944PNRC2ENSG00000189266.7T>C2.6746e-2192345Anterior_cingulate_cortex

meQTL of rs7540557 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 )
chr12434502424345901E069-32043
chr12434601524346116E069-31828
chr12434502424345901E070-32043
chr12437267624373198E070-4746
chr12437324124373337E070-4607
chr12439728824397819E07019344
chr12434502424345901E071-32043
chr12439728824397819E07219344
chr12434502424345901E073-32043
chr12434419724344247E081-33697
chr12434428924344347E081-33597
chr12434467124344744E081-33200
chr12434502424345901E081-32043
chr12434601524346116E081-31828
chr12434502424345901E082-32043
chr12437230924372611E082-5333
chr12437267624373198E082-4746
chr12439728824397819E08219344