rs6755573

Homo sapiens
G>A
UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0112 (3378/29980,GnomAD)
G==0110 (3205/29118,TOPMED)
G==0134 (669/5008,1000G)
G==0177 (681/3854,ALSPAC)
G==0190 (705/3708,TWINSUK)
chr2:237986970 (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.237986970G>A
GRCh37.p13 chr 2NC_000002.11:g.238895612G>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
1000GenomesAfricanSub1322G=0.033A=0.967
1000GenomesAmericanSub694G=0.180A=0.820
1000GenomesEast AsianSub1008G=0.030A=0.970
1000GenomesEuropeSub1006G=0.164A=0.836
1000GenomesGlobalStudy-wide5008G=0.134A=0.866
1000GenomesSouth AsianSub978G=0.310A=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.177A=0.823
The Genome Aggregation DatabaseAfricanSub8724G=0.056A=0.944
The Genome Aggregation DatabaseAmericanSub838G=0.170A=0.830
The Genome Aggregation DatabaseEast AsianSub1622G=0.030A=0.970
The Genome Aggregation DatabaseEuropeSub18494G=0.143A=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29980G=0.112A=0.887
The Genome Aggregation DatabaseOtherSub302G=0.110A=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.110A=0.889
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=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
rs67555730.000138alcohol consumption23743675

eQTL of rs6755573 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238895612SCLYENSG00000132330.12G>A7.8532e-10-73918Cerebellum
Chr2:238895612SCLYENSG00000132330.12G>A1.0714e-8-73918Cortex
Chr2:238895612SCLYENSG00000132330.12G>A2.0850e-8-73918Cerebellar_Hemisphere
Chr2:238895612SCLYENSG00000132330.12G>A1.4177e-3-73918Caudate_basal_ganglia
Chr2:238895612SCLYENSG00000132330.12G>A7.2091e-4-73918Anterior_cingulate_cortex

meQTL of rs6755573 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.0680291539545211.8712e-15

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 )
chr2238877816238878038E067-17574
chr2238878398238878539E067-17073
chr2238878551238878601E067-17011
chr2238878666238878738E067-16874
chr2238879158238879263E067-16349
chr2238886584238886634E067-8978
chr2238886907238887414E067-8198
chr2238888018238888228E067-7384
chr2238888415238888465E067-7147
chr2238888921238888998E067-6614
chr2238889558238889737E067-5875
chr2238889976238890179E067-5433
chr2238893121238893238E067-2374
chr2238904560238904874E0678948
chr2238904955238905113E0679343
chr2238917607238917771E06721995
chr2238931681238931768E06736069
chr2238851806238851846E068-43766
chr2238851954238852295E068-43317
chr2238877816238878038E068-17574
chr2238878398238878539E068-17073
chr2238878551238878601E068-17011
chr2238878666238878738E068-16874
chr2238879158238879263E068-16349
chr2238886584238886634E068-8978
chr2238886907238887414E068-8198
chr2238888018238888228E068-7384
chr2238888415238888465E068-7147
chr2238888921238888998E068-6614
chr2238889558238889737E068-5875
chr2238889976238890179E068-5433
chr2238892164238892276E068-3336
chr2238893121238893238E068-2374
chr2238877816238878038E069-17574
chr2238878398238878539E069-17073
chr2238878551238878601E069-17011
chr2238878666238878738E069-16874
chr2238886584238886634E069-8978
chr2238886907238887414E069-8198
chr2238888018238888228E069-7384
chr2238888921238888998E069-6614
chr2238889558238889737E069-5875
chr2238893121238893238E069-2374
chr2238904955238905113E0699343
chr2238918301238918438E06922689
chr2238919370238919610E06923758
chr2238919757238919867E06924145
chr2238928552238929028E06932940
chr2238886584238886634E070-8978
chr2238886907238887414E070-8198
chr2238888921238888998E070-6614
chr2238851806238851846E071-43766
chr2238851954238852295E071-43317
chr2238878666238878738E071-16874
chr2238879158238879263E071-16349
chr2238886011238886062E071-9550
chr2238886584238886634E071-8978
chr2238886907238887414E071-8198
chr2238888018238888228E071-7384
chr2238888415238888465E071-7147
chr2238888921238888998E071-6614
chr2238893121238893238E071-2374
chr2238917607238917771E07121995
chr2238917904238917968E07122292
chr2238918301238918438E07122689
chr2238919370238919610E07123758
chr2238919757238919867E07124145
chr2238867147238867197E072-28415
chr2238878551238878601E072-17011
chr2238886011238886062E072-9550
chr2238886584238886634E072-8978
chr2238886907238887414E072-8198
chr2238888018238888228E072-7384
chr2238888415238888465E072-7147
chr2238888921238888998E072-6614
chr2238889558238889737E072-5875
chr2238893121238893238E072-2374
chr2238917607238917771E07221995
chr2238878551238878601E073-17011
chr2238878666238878738E073-16874
chr2238886011238886062E073-9550
chr2238886584238886634E073-8978
chr2238886907238887414E073-8198
chr2238888018238888228E073-7384
chr2238888415238888465E073-7147
chr2238888921238888998E073-6614
chr2238889558238889737E073-5875
chr2238892164238892276E073-3336
chr2238893121238893238E073-2374
chr2238851954238852295E074-43317
chr2238878551238878601E074-17011
chr2238878666238878738E074-16874
chr2238879158238879263E074-16349
chr2238880434238880549E074-15063
chr2238880894238880969E074-14643
chr2238884641238884818E074-10794
chr2238886011238886062E074-9550
chr2238886584238886634E074-8978
chr2238886907238887414E074-8198
chr2238888921238888998E074-6614
chr2238889558238889737E074-5875
chr2238889976238890179E074-5433
chr2238893121238893238E074-2374
chr2238904560238904874E0748948
chr2238904955238905113E0749343
chr2238915164238915422E07419552
chr2238917607238917771E07421995
chr2238917904238917968E07422292
chr2238918301238918438E07422689
chr2238919370238919610E07423758
chr2238919757238919867E07424145
chr2238931681238931768E07436069
chr2238877816238878038E081-17574
chr2238878398238878539E081-17073
chr2238886907238887414E082-8198










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238874796238876104E067-19508
chr2238876111238876550E067-19062
chr2238864688238864740E068-30872
chr2238864741238864973E068-30639
chr2238865051238865134E068-30478
chr2238865144238865248E068-30364
chr2238874796238876104E068-19508
chr2238876111238876550E068-19062
chr2238865051238865134E069-30478
chr2238865144238865248E069-30364
chr2238874796238876104E069-19508
chr2238876111238876550E069-19062
chr2238864741238864973E070-30639
chr2238874796238876104E070-19508
chr2238876111238876550E070-19062
chr2238874796238876104E071-19508
chr2238876111238876550E071-19062
chr2238874796238876104E072-19508
chr2238876111238876550E072-19062
chr2238865051238865134E073-30478
chr2238865144238865248E073-30364
chr2238874796238876104E073-19508
chr2238876111238876550E073-19062
chr2238874796238876104E074-19508
chr2238876111238876550E074-19062
chr2238876111238876550E081-19062
chr2238864688238864740E082-30872
chr2238864741238864973E082-30639
chr2238865051238865134E082-30478
chr2238865144238865248E082-30364
chr2238874796238876104E082-19508
chr2238876111238876550E082-19062