rs11690668

Homo sapiens
C>T
UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0127 (3818/29848,GnomAD)
C==0134 (3913/29118,TOPMED)
C==0152 (760/5008,1000G)
C==0177 (682/3854,ALSPAC)
C==0190 (705/3708,TWINSUK)
chr2:237988316 (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.237988316C>T
GRCh37.p13 chr 2NC_000002.11:g.238896958C>T

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=0.099T=0.901
1000GenomesAmericanSub694C=0.180T=0.820
1000GenomesEast AsianSub1008C=0.030T=0.970
1000GenomesEuropeSub1006C=0.164T=0.836
1000GenomesGlobalStudy-wide5008C=0.152T=0.848
1000GenomesSouth AsianSub978C=0.310T=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.177T=0.823
The Genome Aggregation DatabaseAfricanSub8694C=0.108T=0.892
The Genome Aggregation DatabaseAmericanSub838C=0.170T=0.830
The Genome Aggregation DatabaseEast AsianSub1618C=0.029T=0.971
The Genome Aggregation DatabaseEuropeSub18396C=0.144T=0.855
The Genome Aggregation DatabaseGlobalStudy-wide29848C=0.127T=0.872
The Genome Aggregation DatabaseOtherSub302C=0.110T=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.134T=0.865
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.190T=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
rs116906680.000143alcohol consumption23743675

eQTL of rs11690668 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238896958SCLYENSG00000132330.12C>T7.8532e-10-72572Cerebellum
Chr2:238896958SCLYENSG00000132330.12C>T1.0714e-8-72572Cortex
Chr2:238896958SCLYENSG00000132330.12C>T2.0850e-8-72572Cerebellar_Hemisphere
Chr2:238896958SCLYENSG00000132330.12C>T1.4177e-3-72572Caudate_basal_ganglia
Chr2:238896958SCLYENSG00000132330.12C>T2.3006e-3-72572Substantia_nigra
Chr2:238896958SCLYENSG00000132330.12C>T7.2091e-4-72572Anterior_cingulate_cortex

meQTL of rs11690668 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.06462263479058882.4442e-14

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 )
chr2238877816238878038E067-18920
chr2238878398238878539E067-18419
chr2238878551238878601E067-18357
chr2238878666238878738E067-18220
chr2238879158238879263E067-17695
chr2238886584238886634E067-10324
chr2238886907238887414E067-9544
chr2238888018238888228E067-8730
chr2238888415238888465E067-8493
chr2238888921238888998E067-7960
chr2238889558238889737E067-7221
chr2238889976238890179E067-6779
chr2238893121238893238E067-3720
chr2238904560238904874E0677602
chr2238904955238905113E0677997
chr2238917607238917771E06720649
chr2238931681238931768E06734723
chr2238851806238851846E068-45112
chr2238851954238852295E068-44663
chr2238877816238878038E068-18920
chr2238878398238878539E068-18419
chr2238878551238878601E068-18357
chr2238878666238878738E068-18220
chr2238879158238879263E068-17695
chr2238886584238886634E068-10324
chr2238886907238887414E068-9544
chr2238888018238888228E068-8730
chr2238888415238888465E068-8493
chr2238888921238888998E068-7960
chr2238889558238889737E068-7221
chr2238889976238890179E068-6779
chr2238892164238892276E068-4682
chr2238893121238893238E068-3720
chr2238877816238878038E069-18920
chr2238878398238878539E069-18419
chr2238878551238878601E069-18357
chr2238878666238878738E069-18220
chr2238886584238886634E069-10324
chr2238886907238887414E069-9544
chr2238888018238888228E069-8730
chr2238888921238888998E069-7960
chr2238889558238889737E069-7221
chr2238893121238893238E069-3720
chr2238904955238905113E0697997
chr2238918301238918438E06921343
chr2238919370238919610E06922412
chr2238919757238919867E06922799
chr2238928552238929028E06931594
chr2238886584238886634E070-10324
chr2238886907238887414E070-9544
chr2238888921238888998E070-7960
chr2238851806238851846E071-45112
chr2238851954238852295E071-44663
chr2238878666238878738E071-18220
chr2238879158238879263E071-17695
chr2238886011238886062E071-10896
chr2238886584238886634E071-10324
chr2238886907238887414E071-9544
chr2238888018238888228E071-8730
chr2238888415238888465E071-8493
chr2238888921238888998E071-7960
chr2238893121238893238E071-3720
chr2238917607238917771E07120649
chr2238917904238917968E07120946
chr2238918301238918438E07121343
chr2238919370238919610E07122412
chr2238919757238919867E07122799
chr2238867147238867197E072-29761
chr2238878551238878601E072-18357
chr2238886011238886062E072-10896
chr2238886584238886634E072-10324
chr2238886907238887414E072-9544
chr2238888018238888228E072-8730
chr2238888415238888465E072-8493
chr2238888921238888998E072-7960
chr2238889558238889737E072-7221
chr2238893121238893238E072-3720
chr2238917607238917771E07220649
chr2238878551238878601E073-18357
chr2238878666238878738E073-18220
chr2238886011238886062E073-10896
chr2238886584238886634E073-10324
chr2238886907238887414E073-9544
chr2238888018238888228E073-8730
chr2238888415238888465E073-8493
chr2238888921238888998E073-7960
chr2238889558238889737E073-7221
chr2238892164238892276E073-4682
chr2238893121238893238E073-3720
chr2238851954238852295E074-44663
chr2238878551238878601E074-18357
chr2238878666238878738E074-18220
chr2238879158238879263E074-17695
chr2238880434238880549E074-16409
chr2238880894238880969E074-15989
chr2238884641238884818E074-12140
chr2238886011238886062E074-10896
chr2238886584238886634E074-10324
chr2238886907238887414E074-9544
chr2238888921238888998E074-7960
chr2238889558238889737E074-7221
chr2238889976238890179E074-6779
chr2238893121238893238E074-3720
chr2238904560238904874E0747602
chr2238904955238905113E0747997
chr2238915164238915422E07418206
chr2238917607238917771E07420649
chr2238917904238917968E07420946
chr2238918301238918438E07421343
chr2238919370238919610E07422412
chr2238919757238919867E07422799
chr2238931681238931768E07434723
chr2238877816238878038E081-18920
chr2238878398238878539E081-18419
chr2238886907238887414E082-9544










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238874796238876104E067-20854
chr2238876111238876550E067-20408
chr2238864688238864740E068-32218
chr2238864741238864973E068-31985
chr2238865051238865134E068-31824
chr2238865144238865248E068-31710
chr2238874796238876104E068-20854
chr2238876111238876550E068-20408
chr2238865051238865134E069-31824
chr2238865144238865248E069-31710
chr2238874796238876104E069-20854
chr2238876111238876550E069-20408
chr2238864741238864973E070-31985
chr2238874796238876104E070-20854
chr2238876111238876550E070-20408
chr2238874796238876104E071-20854
chr2238876111238876550E071-20408
chr2238874796238876104E072-20854
chr2238876111238876550E072-20408
chr2238865051238865134E073-31824
chr2238865144238865248E073-31710
chr2238874796238876104E073-20854
chr2238876111238876550E073-20408
chr2238874796238876104E074-20854
chr2238876111238876550E074-20408
chr2238876111238876550E081-20408
chr2238864688238864740E082-32218
chr2238864741238864973E082-31985
chr2238865051238865134E082-31824
chr2238865144238865248E082-31710
chr2238874796238876104E082-20854
chr2238876111238876550E082-20408