rs6553017

Homo sapiens
G>T
FAT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0336 (10052/29892,GnomAD)
G==0301 (8788/29118,TOPMED)
G==0365 (1828/5008,1000G)
G==0431 (1660/3854,ALSPAC)
G==0419 (1554/3708,TWINSUK)
chr4:186660322 (GRCh38.p7) (4q35.2)
ND
GWASdb2
1   publication(s)
See rs on genome
85 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.186660322G>T
GRCh37.p13 chr 4NC_000004.11:g.187581476G>T
FAT1 RefSeqGeneNG_046994.1:g.71594C>A

Gene: FAT1, FAT atypical cadherin 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
FAT1 transcriptNM_005245.3:c.N/AIntron Variant
FAT1 transcript variant X1XM_005262834.2:c.N/AIntron Variant
FAT1 transcript variant X2XM_005262835.2:c.N/AIntron Variant
FAT1 transcript variant X3XM_006714139.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.107T=0.893
1000GenomesAmericanSub694G=0.390T=0.610
1000GenomesEast AsianSub1008G=0.435T=0.565
1000GenomesEuropeSub1006G=0.431T=0.569
1000GenomesGlobalStudy-wide5008G=0.365T=0.635
1000GenomesSouth AsianSub978G=0.560T=0.440
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.431T=0.569
The Genome Aggregation DatabaseAfricanSub8704G=0.139T=0.861
The Genome Aggregation DatabaseAmericanSub836G=0.390T=0.610
The Genome Aggregation DatabaseEast AsianSub1612G=0.423T=0.577
The Genome Aggregation DatabaseEuropeSub18440G=0.419T=0.580
The Genome Aggregation DatabaseGlobalStudy-wide29892G=0.336T=0.663
The Genome Aggregation DatabaseOtherSub300G=0.360T=0.640
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.301T=0.698
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.419T=0.581
PMID Title Author Journal
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs65530175.5E-06alcohol and nictotine co-dependence22488850

eQTL of rs6553017 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 rs6553017 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 )
chr4187603858187604043E06722382
chr4187621139187621319E06739663
chr4187621546187621633E06740070
chr4187565909187566332E068-15144
chr4187579012187579240E068-2236
chr4187597575187598212E06816099
chr4187605610187605709E06824134
chr4187605927187606027E06824451
chr4187606138187606370E06824662
chr4187614283187614492E06832807
chr4187614656187615016E06833180
chr4187621139187621319E06839663
chr4187621546187621633E06840070
chr4187622966187623048E06841490
chr4187623195187623343E06841719
chr4187623398187623481E06841922
chr4187623577187624067E06842101
chr4187579012187579240E069-2236
chr4187590269187591383E0698793
chr4187597575187598212E06916099
chr4187606851187607392E06925375
chr4187609321187609767E06927845
chr4187609886187609960E06928410
chr4187621546187621633E06940070
chr4187621748187622329E06940272
chr4187622362187622953E06940886
chr4187545228187545372E070-36104
chr4187605610187605709E07024134
chr4187605927187606027E07024451
chr4187606138187606370E07024662
chr4187606541187606610E07025065
chr4187606687187606767E07025211
chr4187606851187607392E07025375
chr4187616406187616668E07034930
chr4187616737187616817E07035261
chr4187621139187621319E07039663
chr4187621546187621633E07040070
chr4187622966187623048E07041490
chr4187623195187623343E07041719
chr4187623398187623481E07041922
chr4187623577187624067E07042101
chr4187565909187566332E071-15144
chr4187579012187579240E071-2236
chr4187579408187579458E071-2018
chr4187579558187579633E071-1843
chr4187593640187593691E07112164
chr4187606851187607392E07125375
chr4187609321187609767E07127845
chr4187609886187609960E07128410
chr4187621139187621319E07139663
chr4187621546187621633E07140070
chr4187622966187623048E07141490
chr4187565909187566332E072-15144
chr4187579012187579240E072-2236
chr4187614283187614492E07232807
chr4187614656187615016E07233180
chr4187623195187623343E07241719
chr4187614283187614492E07332807
chr4187614656187615016E07333180
chr4187623398187623481E07341922
chr4187544752187544980E074-36496
chr4187545118187545172E074-36304
chr4187565701187565777E074-15699
chr4187565909187566332E074-15144
chr4187579012187579240E074-2236
chr4187579408187579458E074-2018
chr4187579558187579633E074-1843
chr4187606851187607392E07425375
chr4187609321187609767E07427845
chr4187622362187622953E07440886
chr4187622966187623048E07441490
chr4187623195187623343E07441719
chr4187624495187624585E07443019
chr4187624764187624901E07443288
chr4187621748187622329E08140272
chr4187622362187622953E08140886
chr4187622966187623048E08141490
chr4187623195187623343E08141719
chr4187623398187623481E08141922
chr4187623577187624067E08142101
chr4187621748187622329E08240272
chr4187622362187622953E08240886
chr4187622966187623048E08241490
chr4187623577187624067E08242101
chr4187624495187624585E08243019










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr4187572393187572674E067-8802
chr4187572732187573259E067-8217
chr4187572393187572674E068-8802
chr4187572732187573259E068-8217
chr4187572393187572674E069-8802
chr4187572732187573259E069-8217
chr4187572393187572674E070-8802
chr4187572732187573259E070-8217
chr4187572393187572674E071-8802
chr4187572732187573259E071-8217
chr4187572393187572674E072-8802
chr4187572732187573259E072-8217
chr4187572393187572674E073-8802
chr4187572732187573259E073-8217
chr4187572393187572674E074-8802
chr4187572732187573259E074-8217
chr4187572732187573259E081-8217
chr4187572393187572674E082-8802
chr4187572732187573259E082-8217