rs1557978

Homo sapiens
C>T
LOC105375147 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0291 (8698/29864,GnomAD)
T==0256 (7458/29118,TOPMED)
T==0270 (1354/5008,1000G)
T==0347 (1336/3854,ALSPAC)
T==0341 (1264/3708,TWINSUK)
chr7:9926280 (GRCh38.p7) (7p21.3)
AD
GWASdb2
2   publication(s)
See rs on genome
23 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.9926280C>T
GRCh37.p13 chr 7NC_000007.13:g.9965912T>C

Gene: LOC105375147, uncharacterized LOC105375147(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105375147 transcriptXR_927026.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.154C==0.846
1000GenomesAmericanSub694T=0.290C==0.710
1000GenomesEast AsianSub1008T=0.276C==0.724
1000GenomesEuropeSub1006T=0.359C==0.641
1000GenomesGlobalStudy-wide5008T=0.270C==0.730
1000GenomesSouth AsianSub978T=0.320C==0.680
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.347C==0.653
The Genome Aggregation DatabaseAfricanSub8706T=0.196C==0.804
The Genome Aggregation DatabaseAmericanSub834T=0.310C==0.690
The Genome Aggregation DatabaseEast AsianSub1608T=0.246C==0.754
The Genome Aggregation DatabaseEuropeSub18416T=0.338C==0.661
The Genome Aggregation DatabaseGlobalStudy-wide29864T=0.291C==0.708
The Genome Aggregation DatabaseOtherSub300T=0.330C==0.670
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.256C==0.743
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.341C==0.659
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry
17903296Genome-wide association with bone mass and geometry in the Framingham Heart Study.Kiel DPBMC Med Genet

P-Value

SNP ID p-value Traits Study
rs15579787.1E-05alcoholism (heaviness of drinking)21529783

eQTL of rs1557978 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 rs1557978 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 )
chr799773779977432E06811465
chr799773779977432E06911465
chr799839529984007E06918040
chr799848059985126E06918893
chr799851649985224E06919252
chr799854569985516E06919544
chr799855939985822E06919681
chr799833929983487E07117480
chr799839529984007E07118040
chr799848059985126E07118893
chr799851649985224E07119252
chr799854569985516E07119544
chr799855939985822E07119681
chr799772579977337E07211345
chr799773779977432E07211465
chr799776559978369E07211743
chr799788829979086E07212970
chr799773779977432E07411465
chr799788829979086E07412970
chr799848059985126E07418893
chr799851649985224E07419252
chr799854569985516E07419544
chr799855939985822E07419681