rs6754093

Homo sapiens
C>A
UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0122 (3642/29828,GnomAD)
C==0125 (3649/29118,TOPMED)
C==0143 (717/5008,1000G)
C==0176 (679/3854,ALSPAC)
C==0190 (706/3708,TWINSUK)
chr2:237974093 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
120 Enhancers around
32 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.237974093C>A
GRCh37.p13 chr 2NC_000002.11:g.238882735C>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
1000GenomesAfricanSub1322C=0.070A=0.930
1000GenomesAmericanSub694C=0.180A=0.820
1000GenomesEast AsianSub1008C=0.030A=0.970
1000GenomesEuropeSub1006C=0.164A=0.836
1000GenomesGlobalStudy-wide5008C=0.143A=0.857
1000GenomesSouth AsianSub978C=0.310A=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.176A=0.824
The Genome Aggregation DatabaseAfricanSub8708C=0.089A=0.911
The Genome Aggregation DatabaseAmericanSub826C=0.180A=0.820
The Genome Aggregation DatabaseEast AsianSub1622C=0.030A=0.970
The Genome Aggregation DatabaseEuropeSub18370C=0.143A=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29828C=0.122A=0.877
The Genome Aggregation DatabaseOtherSub302C=0.110A=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.125A=0.874
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=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
rs67540930.000139alcohol consumption23743675

eQTL of rs6754093 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238882735SCLYENSG00000132330.12C>A7.8532e-10-86795Cerebellum
Chr2:238882735SCLYENSG00000132330.12C>A1.0714e-8-86795Cortex
Chr2:238882735SCLYENSG00000132330.12C>A2.0850e-8-86795Cerebellar_Hemisphere
Chr2:238882735SCLYENSG00000132330.12C>A1.4177e-3-86795Caudate_basal_ganglia
Chr2:238882735SCLYENSG00000132330.12C>A2.3006e-3-86795Substantia_nigra
Chr2:238882735SCLYENSG00000132330.12C>A7.2091e-4-86795Anterior_cingulate_cortex

meQTL of rs6754093 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.06670119019215933.7259e-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 )
chr2238834367238834417E067-48318
chr2238877816238878038E067-4697
chr2238878398238878539E067-4196
chr2238878551238878601E067-4134
chr2238878666238878738E067-3997
chr2238879158238879263E067-3472
chr2238886584238886634E0673849
chr2238886907238887414E0674172
chr2238888018238888228E0675283
chr2238888415238888465E0675680
chr2238888921238888998E0676186
chr2238889558238889737E0676823
chr2238889976238890179E0677241
chr2238893121238893238E06710386
chr2238904560238904874E06721825
chr2238904955238905113E06722220
chr2238917607238917771E06734872
chr2238931681238931768E06748946
chr2238851806238851846E068-30889
chr2238851954238852295E068-30440
chr2238877816238878038E068-4697
chr2238878398238878539E068-4196
chr2238878551238878601E068-4134
chr2238878666238878738E068-3997
chr2238879158238879263E068-3472
chr2238886584238886634E0683849
chr2238886907238887414E0684172
chr2238888018238888228E0685283
chr2238888415238888465E0685680
chr2238888921238888998E0686186
chr2238889558238889737E0686823
chr2238889976238890179E0687241
chr2238892164238892276E0689429
chr2238893121238893238E06810386
chr2238840070238840408E069-42327
chr2238877816238878038E069-4697
chr2238878398238878539E069-4196
chr2238878551238878601E069-4134
chr2238878666238878738E069-3997
chr2238886584238886634E0693849
chr2238886907238887414E0694172
chr2238888018238888228E0695283
chr2238888921238888998E0696186
chr2238889558238889737E0696823
chr2238893121238893238E06910386
chr2238904955238905113E06922220
chr2238918301238918438E06935566
chr2238919370238919610E06936635
chr2238919757238919867E06937022
chr2238928552238929028E06945817
chr2238886584238886634E0703849
chr2238886907238887414E0704172
chr2238888921238888998E0706186
chr2238840070238840408E071-42327
chr2238851806238851846E071-30889
chr2238851954238852295E071-30440
chr2238878666238878738E071-3997
chr2238879158238879263E071-3472
chr2238886011238886062E0713276
chr2238886584238886634E0713849
chr2238886907238887414E0714172
chr2238888018238888228E0715283
chr2238888415238888465E0715680
chr2238888921238888998E0716186
chr2238893121238893238E07110386
chr2238917607238917771E07134872
chr2238917904238917968E07135169
chr2238918301238918438E07135566
chr2238919370238919610E07136635
chr2238919757238919867E07137022
chr2238867147238867197E072-15538
chr2238878551238878601E072-4134
chr2238886011238886062E0723276
chr2238886584238886634E0723849
chr2238886907238887414E0724172
chr2238888018238888228E0725283
chr2238888415238888465E0725680
chr2238888921238888998E0726186
chr2238889558238889737E0726823
chr2238893121238893238E07210386
chr2238917607238917771E07234872
chr2238840070238840408E073-42327
chr2238878551238878601E073-4134
chr2238878666238878738E073-3997
chr2238886011238886062E0733276
chr2238886584238886634E0733849
chr2238886907238887414E0734172
chr2238888018238888228E0735283
chr2238888415238888465E0735680
chr2238888921238888998E0736186
chr2238889558238889737E0736823
chr2238892164238892276E0739429
chr2238893121238893238E07310386
chr2238840070238840408E074-42327
chr2238851954238852295E074-30440
chr2238878551238878601E074-4134
chr2238878666238878738E074-3997
chr2238879158238879263E074-3472
chr2238880434238880549E074-2186
chr2238880894238880969E074-1766
chr2238884641238884818E0741906
chr2238886011238886062E0743276
chr2238886584238886634E0743849
chr2238886907238887414E0744172
chr2238888921238888998E0746186
chr2238889558238889737E0746823
chr2238889976238890179E0747241
chr2238893121238893238E07410386
chr2238904560238904874E07421825
chr2238904955238905113E07422220
chr2238915164238915422E07432429
chr2238917607238917771E07434872
chr2238917904238917968E07435169
chr2238918301238918438E07435566
chr2238919370238919610E07436635
chr2238919757238919867E07437022
chr2238931681238931768E07448946
chr2238877816238878038E081-4697
chr2238878398238878539E081-4196
chr2238886907238887414E0824172










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238874796238876104E067-6631
chr2238876111238876550E067-6185
chr2238864688238864740E068-17995
chr2238864741238864973E068-17762
chr2238865051238865134E068-17601
chr2238865144238865248E068-17487
chr2238874796238876104E068-6631
chr2238876111238876550E068-6185
chr2238865051238865134E069-17601
chr2238865144238865248E069-17487
chr2238874796238876104E069-6631
chr2238876111238876550E069-6185
chr2238864741238864973E070-17762
chr2238874796238876104E070-6631
chr2238876111238876550E070-6185
chr2238874796238876104E071-6631
chr2238876111238876550E071-6185
chr2238874796238876104E072-6631
chr2238876111238876550E072-6185
chr2238865051238865134E073-17601
chr2238865144238865248E073-17487
chr2238874796238876104E073-6631
chr2238876111238876550E073-6185
chr2238874796238876104E074-6631
chr2238876111238876550E074-6185
chr2238876111238876550E081-6185
chr2238864688238864740E082-17995
chr2238864741238864973E082-17762
chr2238865051238865134E082-17601
chr2238865144238865248E082-17487
chr2238874796238876104E082-6631
chr2238876111238876550E082-6185