rs7572717

Homo sapiens
T>A
UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0151 (4137/27282,GnomAD)
T==0178 (891/5008,1000G)
T==0177 (683/3854,ALSPAC)
T==0190 (706/3708,TWINSUK)
chr2:237981674 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
115 Enhancers around
32 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.237981674T>A
GRCh37.p13 chr 2NC_000002.11:g.238890316T>A

Gene: UBE2F, ubiquitin conjugating enzyme E2 F (putative)(plus strand)

Molecule type Change Amino acid[Codon] SO Term
UBE2F transcript variant 2NM_001278305.1:c.N/AIntron Variant
UBE2F transcript variant 3NM_001278306.1:c.N/AIntron Variant
UBE2F transcript variant 4NM_001278307.1:c.N/AIntron Variant
UBE2F transcript variant 5NM_001278308.1:c.N/AIntron Variant
UBE2F transcript variant 1NM_080678.2:c.N/AIntron Variant
UBE2F transcript variant 6NR_103498.1:n.N/AIntron Variant
UBE2F transcript variant 7NR_103499.1:n.N/AIntron Variant
UBE2F transcript variant 8NR_103500.1:n.N/AIntron Variant

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand)

Molecule type Change Amino acid[Codon] SO Term
UBE2F-SCLY transcriptNR_037904.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.197A=0.803
1000GenomesAmericanSub694T=0.180A=0.820
1000GenomesEast AsianSub1008T=0.030A=0.970
1000GenomesEuropeSub1006T=0.164A=0.836
1000GenomesGlobalStudy-wide5008T=0.178A=0.822
1000GenomesSouth AsianSub978T=0.310A=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.177A=0.823
The Genome Aggregation DatabaseAfricanSub7954T=0.187A=0.813
The Genome Aggregation DatabaseAmericanSub770T=0.170A=0.830
The Genome Aggregation DatabaseEast AsianSub1542T=0.029A=0.971
The Genome Aggregation DatabaseEuropeSub16724T=0.145A=0.854
The Genome Aggregation DatabaseGlobalStudy-wide27282T=0.151A=0.848
The Genome Aggregation DatabaseOtherSub292T=0.110A=0.890
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.190A=0.810
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
rs75727170.00015alcohol consumption23743675

eQTL of rs7572717 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238890316SCLYENSG00000132330.12T>A7.8532e-10-79214Cerebellum
Chr2:238890316SCLYENSG00000132330.12T>A2.8719e-4-79214Frontal_Cortex_BA9
Chr2:238890316SCLYENSG00000132330.12T>A1.0714e-8-79214Cortex
Chr2:238890316SCLYENSG00000132330.12T>A2.0850e-8-79214Cerebellar_Hemisphere
Chr2:238890316SCLYENSG00000132330.12T>A1.4177e-3-79214Caudate_basal_ganglia
Chr2:238890316SCLYENSG00000132330.12T>A2.3006e-3-79214Substantia_nigra
Chr2:238890316SCLYENSG00000132330.12T>A7.2091e-4-79214Anterior_cingulate_cortex

meQTL of rs7572717 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.05796513412091165.6486e-12

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 )
chr2238877816238878038E067-12278
chr2238878398238878539E067-11777
chr2238878551238878601E067-11715
chr2238878666238878738E067-11578
chr2238879158238879263E067-11053
chr2238886584238886634E067-3682
chr2238886907238887414E067-2902
chr2238888018238888228E067-2088
chr2238888415238888465E067-1851
chr2238888921238888998E067-1318
chr2238889558238889737E067-579
chr2238889976238890179E067-137
chr2238893121238893238E0672805
chr2238904560238904874E06714244
chr2238904955238905113E06714639
chr2238917607238917771E06727291
chr2238931681238931768E06741365
chr2238851806238851846E068-38470
chr2238851954238852295E068-38021
chr2238877816238878038E068-12278
chr2238878398238878539E068-11777
chr2238878551238878601E068-11715
chr2238878666238878738E068-11578
chr2238879158238879263E068-11053
chr2238886584238886634E068-3682
chr2238886907238887414E068-2902
chr2238888018238888228E068-2088
chr2238888415238888465E068-1851
chr2238888921238888998E068-1318
chr2238889558238889737E068-579
chr2238889976238890179E068-137
chr2238892164238892276E0681848
chr2238893121238893238E0682805
chr2238877816238878038E069-12278
chr2238878398238878539E069-11777
chr2238878551238878601E069-11715
chr2238878666238878738E069-11578
chr2238886584238886634E069-3682
chr2238886907238887414E069-2902
chr2238888018238888228E069-2088
chr2238888921238888998E069-1318
chr2238889558238889737E069-579
chr2238893121238893238E0692805
chr2238904955238905113E06914639
chr2238918301238918438E06927985
chr2238919370238919610E06929054
chr2238919757238919867E06929441
chr2238928552238929028E06938236
chr2238886584238886634E070-3682
chr2238886907238887414E070-2902
chr2238888921238888998E070-1318
chr2238851806238851846E071-38470
chr2238851954238852295E071-38021
chr2238878666238878738E071-11578
chr2238879158238879263E071-11053
chr2238886011238886062E071-4254
chr2238886584238886634E071-3682
chr2238886907238887414E071-2902
chr2238888018238888228E071-2088
chr2238888415238888465E071-1851
chr2238888921238888998E071-1318
chr2238893121238893238E0712805
chr2238917607238917771E07127291
chr2238917904238917968E07127588
chr2238918301238918438E07127985
chr2238919370238919610E07129054
chr2238919757238919867E07129441
chr2238867147238867197E072-23119
chr2238878551238878601E072-11715
chr2238886011238886062E072-4254
chr2238886584238886634E072-3682
chr2238886907238887414E072-2902
chr2238888018238888228E072-2088
chr2238888415238888465E072-1851
chr2238888921238888998E072-1318
chr2238889558238889737E072-579
chr2238893121238893238E0722805
chr2238917607238917771E07227291
chr2238878551238878601E073-11715
chr2238878666238878738E073-11578
chr2238886011238886062E073-4254
chr2238886584238886634E073-3682
chr2238886907238887414E073-2902
chr2238888018238888228E073-2088
chr2238888415238888465E073-1851
chr2238888921238888998E073-1318
chr2238889558238889737E073-579
chr2238892164238892276E0731848
chr2238893121238893238E0732805
chr2238851954238852295E074-38021
chr2238878551238878601E074-11715
chr2238878666238878738E074-11578
chr2238879158238879263E074-11053
chr2238880434238880549E074-9767
chr2238880894238880969E074-9347
chr2238884641238884818E074-5498
chr2238886011238886062E074-4254
chr2238886584238886634E074-3682
chr2238886907238887414E074-2902
chr2238888921238888998E074-1318
chr2238889558238889737E074-579
chr2238889976238890179E074-137
chr2238893121238893238E0742805
chr2238904560238904874E07414244
chr2238904955238905113E07414639
chr2238915164238915422E07424848
chr2238917607238917771E07427291
chr2238917904238917968E07427588
chr2238918301238918438E07427985
chr2238919370238919610E07429054
chr2238919757238919867E07429441
chr2238931681238931768E07441365
chr2238877816238878038E081-12278
chr2238878398238878539E081-11777
chr2238886907238887414E082-2902










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238874796238876104E067-14212
chr2238876111238876550E067-13766
chr2238864688238864740E068-25576
chr2238864741238864973E068-25343
chr2238865051238865134E068-25182
chr2238865144238865248E068-25068
chr2238874796238876104E068-14212
chr2238876111238876550E068-13766
chr2238865051238865134E069-25182
chr2238865144238865248E069-25068
chr2238874796238876104E069-14212
chr2238876111238876550E069-13766
chr2238864741238864973E070-25343
chr2238874796238876104E070-14212
chr2238876111238876550E070-13766
chr2238874796238876104E071-14212
chr2238876111238876550E071-13766
chr2238874796238876104E072-14212
chr2238876111238876550E072-13766
chr2238865051238865134E073-25182
chr2238865144238865248E073-25068
chr2238874796238876104E073-14212
chr2238876111238876550E073-13766
chr2238874796238876104E074-14212
chr2238876111238876550E074-13766
chr2238876111238876550E081-13766
chr2238864688238864740E082-25576
chr2238864741238864973E082-25343
chr2238865051238865134E082-25182
chr2238865144238865248E082-25068
chr2238874796238876104E082-14212
chr2238876111238876550E082-13766