rs2250045

Homo sapiens
C>T
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0138 (4156/29938,GnomAD)
C==0148 (4332/29118,TOPMED)
C==0165 (824/5008,1000G)
C==0177 (681/3854,ALSPAC)
C==0189 (701/3708,TWINSUK)
chr2:238062221 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
47 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238062221C>T
GRCh37.p13 chr 2NC_000002.11:g.238970862C>T

Gene: SCLY, selenocysteine lyase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SCLY transcriptNM_016510.5:c.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=0.151T=0.849
1000GenomesAmericanSub694C=0.180T=0.820
1000GenomesEast AsianSub1008C=0.029T=0.971
1000GenomesEuropeSub1006C=0.163T=0.837
1000GenomesGlobalStudy-wide5008C=0.165T=0.835
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 DatabaseAfricanSub8710C=0.148T=0.852
The Genome Aggregation DatabaseAmericanSub838C=0.180T=0.820
The Genome Aggregation DatabaseEast AsianSub1616C=0.025T=0.975
The Genome Aggregation DatabaseEuropeSub18472C=0.143T=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29938C=0.138T=0.861
The Genome Aggregation DatabaseOtherSub302C=0.100T=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.148T=0.851
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.189T=0.811
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
rs22500457.04E-05alcohol consumption23743675

eQTL of rs2250045 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238970862SCLYENSG00000132330.12C>T7.8532e-101332Cerebellum
Chr2:238970862SCLYENSG00000132330.12C>T1.0714e-81332Cortex
Chr2:238970862SCLYENSG00000132330.12C>T2.0850e-81332Cerebellar_Hemisphere
Chr2:238970862SCLYENSG00000132330.12C>T1.4177e-31332Caudate_basal_ganglia
Chr2:238970862SCLYENSG00000132330.12C>T7.2091e-41332Anterior_cingulate_cortex

meQTL of rs2250045 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 )
chr2238931681238931768E067-39094
chr2238950342238950447E067-20415
chr2238951505238951913E067-18949
chr2238970839238970899E0670
chr2238990205238990255E06719343
chr2238990452238990751E06719590
chr2238970839238970899E0680
chr2239017313239017876E06846451
chr2238928552238929028E069-41834
chr2238951505238951913E069-18949
chr2238970839238970899E0690
chr2238989790238989866E06918928
chr2238989941238990032E06919079
chr2238990205238990255E06919343
chr2238970839238970899E0700
chr2238950342238950447E071-20415
chr2238951505238951913E071-18949
chr2238951961238952020E071-18842
chr2238970839238970899E0710
chr2238989247238989354E07118385
chr2238989790238989866E07118928
chr2238989941238990032E07119079
chr2238990205238990255E07119343
chr2238990452238990751E07119590
chr2239007116239007529E07136254
chr2239017176239017226E07146314
chr2239017313239017876E07146451
chr2238950342238950447E072-20415
chr2238989790238989866E07218928
chr2238989941238990032E07219079
chr2238990205238990255E07219343
chr2238990452238990751E07219590
chr2239014417239014467E07243555
chr2239014951239015001E07244089
chr2238970839238970899E0730
chr2239014951239015001E07344089
chr2238931681238931768E074-39094
chr2238950342238950447E074-20415
chr2238951505238951913E074-18949
chr2238989790238989866E07418928
chr2238989941238990032E07419079
chr2238990452238990751E07419590
chr2239017313239017876E07446451
chr2238994008238994058E08123146
chr2238994372238994803E08123510
chr2238993565238993671E08222703
chr2238994008238994058E08223146










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-255
chr2238968700238970607E068-255
chr2238968700238970607E069-255
chr2238968700238970607E070-255
chr2238968700238970607E071-255
chr2238968700238970607E072-255
chr2238968700238970607E073-255
chr2238968700238970607E074-255
chr2238968700238970607E081-255
chr2238968700238970607E082-255