rs821488

Homo sapiens
T>C
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0139 (4155/29902,GnomAD)
T==0148 (4330/29118,TOPMED)
T==0164 (821/5008,1000G)
T==0176 (680/3854,ALSPAC)
T==0190 (703/3708,TWINSUK)
chr2:238055115 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
56 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238055115T>C
GRCh37.p13 chr 2NC_000002.11:g.238963756T>C

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=0.148C=0.852
1000GenomesAmericanSub694T=0.180C=0.820
1000GenomesEast AsianSub1008T=0.029C=0.971
1000GenomesEuropeSub1006T=0.165C=0.835
1000GenomesGlobalStudy-wide5008T=0.164C=0.836
1000GenomesSouth AsianSub978T=0.310C=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.176C=0.824
The Genome Aggregation DatabaseAfricanSub8712T=0.146C=0.854
The Genome Aggregation DatabaseAmericanSub838T=0.180C=0.820
The Genome Aggregation DatabaseEast AsianSub1618T=0.025C=0.975
The Genome Aggregation DatabaseEuropeSub18432T=0.144C=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29902T=0.139C=0.861
The Genome Aggregation DatabaseOtherSub302T=0.110C=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.148C=0.851
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.190C=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
rs8214880.000128alcohol consumption23743675

eQTL of rs821488 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238963756SCLYENSG00000132330.12T>C7.8532e-10-5774Cerebellum
Chr2:238963756SCLYENSG00000132330.12T>C1.0714e-8-5774Cortex
Chr2:238963756SCLYENSG00000132330.12T>C2.0850e-8-5774Cerebellar_Hemisphere
Chr2:238963756SCLYENSG00000132330.12T>C1.4177e-3-5774Caudate_basal_ganglia
Chr2:238963756SCLYENSG00000132330.12T>C7.2091e-4-5774Anterior_cingulate_cortex

meQTL of rs821488 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.05953135628673041.2684e-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 )
chr2238917607238917771E067-45985
chr2238931681238931768E067-31988
chr2238950342238950447E067-13309
chr2238951505238951913E067-11843
chr2238970839238970899E0677083
chr2238990205238990255E06726449
chr2238990452238990751E06726696
chr2238970839238970899E0687083
chr2238918301238918438E069-45318
chr2238919370238919610E069-44146
chr2238919757238919867E069-43889
chr2238928552238929028E069-34728
chr2238951505238951913E069-11843
chr2238970839238970899E0697083
chr2238989790238989866E06926034
chr2238989941238990032E06926185
chr2238990205238990255E06926449
chr2238970839238970899E0707083
chr2238917607238917771E071-45985
chr2238917904238917968E071-45788
chr2238918301238918438E071-45318
chr2238919370238919610E071-44146
chr2238919757238919867E071-43889
chr2238950342238950447E071-13309
chr2238951505238951913E071-11843
chr2238951961238952020E071-11736
chr2238970839238970899E0717083
chr2238989247238989354E07125491
chr2238989790238989866E07126034
chr2238989941238990032E07126185
chr2238990205238990255E07126449
chr2238990452238990751E07126696
chr2239007116239007529E07143360
chr2238917607238917771E072-45985
chr2238950342238950447E072-13309
chr2238989790238989866E07226034
chr2238989941238990032E07226185
chr2238990205238990255E07226449
chr2238990452238990751E07226696
chr2238970839238970899E0737083
chr2238915164238915422E074-48334
chr2238917607238917771E074-45985
chr2238917904238917968E074-45788
chr2238918301238918438E074-45318
chr2238919370238919610E074-44146
chr2238919757238919867E074-43889
chr2238931681238931768E074-31988
chr2238950342238950447E074-13309
chr2238951505238951913E074-11843
chr2238989790238989866E07426034
chr2238989941238990032E07426185
chr2238990452238990751E07426696
chr2238994008238994058E08130252
chr2238994372238994803E08130616
chr2238993565238993671E08229809
chr2238994008238994058E08230252










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E0674944
chr2238968700238970607E0684944
chr2238968700238970607E0694944
chr2238968700238970607E0704944
chr2238968700238970607E0714944
chr2238968700238970607E0724944
chr2238968700238970607E0734944
chr2238968700238970607E0744944
chr2238968700238970607E0814944
chr2238968700238970607E0824944