rs3827730

Homo sapiens
T>C
FAF1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0316 (9428/29768,GnomAD)
C=0248 (7220/29118,TOPMED)
C=0375 (1880/5008,1000G)
C=0336 (1294/3854,ALSPAC)
C=0343 (1270/3708,TWINSUK)
chr1:50472176 (GRCh38.p7) (1p32.3)
AD
GWASdb2 | GWASCatalog
5   publication(s)
See rs on genome
2 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.50472176T>C
GRCh37.p13 chr 1NC_000001.10:g.50937848T>C

Gene: FAF1, Fas associated factor 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
FAF1 transcriptNM_007051.2:c.N/AIntron Variant
FAF1 transcript variant X3XM_017000136.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.927C=0.073
1000GenomesAmericanSub694T=0.480C=0.520
1000GenomesEast AsianSub1008T=0.213C=0.787
1000GenomesEuropeSub1006T=0.652C=0.348
1000GenomesGlobalStudy-wide5008T=0.625C=0.375
1000GenomesSouth AsianSub978T=0.720C=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.664C=0.336
The Genome Aggregation DatabaseAfricanSub8662T=0.886C=0.114
The Genome Aggregation DatabaseAmericanSub838T=0.420C=0.580
The Genome Aggregation DatabaseEast AsianSub1606T=0.244C=0.756
The Genome Aggregation DatabaseEuropeSub18360T=0.636C=0.363
The Genome Aggregation DatabaseGlobalStudy-wide29768T=0.683C=0.316
The Genome Aggregation DatabaseOtherSub302T=0.780C=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.752C=0.248
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.657C=0.343
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
21295280FAF1, a gene that is disrupted in cleft palate and has conserved function in zebrafish.Ghassibe-Sabbagh MAm J Hum Genet
22064162Genome-wide association study of comorbid depressive syndrome and alcohol dependence.Edwards ACPsychiatr Genet
26973535Epidemiology, Etiology, and Treatment of Isolated Cleft Palate.Burg MLFront Physiol
21618603Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate.Beaty THGenet Epidemiol

P-Value

SNP ID p-value Traits Study
rs38277300.0000014Alcohol dependence (early age of onset)20201924
rs38277300.00000142alcoholismpha002892
rs38277304.00E-06alcohol dependence22064162
rs38277300.0000408alcoholismpha002893
rs38277300.000041alcohol dependence20201924

eQTL of rs3827730 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 rs3827730 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 )
chr15092737450927559E071-10289
chr15092737450927559E074-10289


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr15088800850889589E067-48259
chr15088800850889589E069-48259
chr15088800850889589E072-48259
chr15088800850889589E073-48259
chr15088800850889589E074-48259
chr15088800850889589E082-48259