rs2262425

Homo sapiens
A>G
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0127 (3806/29936,GnomAD)
A==0129 (3777/29118,TOPMED)
A==0149 (744/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0189 (699/3708,TWINSUK)
chr2:238075488 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238075488A>G
GRCh37.p13 chr 2NC_000002.11:g.238984129A>G

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
1000GenomesAfricanSub1322A=0.091G=0.909
1000GenomesAmericanSub694A=0.180G=0.820
1000GenomesEast AsianSub1008A=0.029G=0.971
1000GenomesEuropeSub1006A=0.162G=0.838
1000GenomesGlobalStudy-wide5008A=0.149G=0.851
1000GenomesSouth AsianSub978A=0.310G=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.176G=0.824
The Genome Aggregation DatabaseAfricanSub8722A=0.109G=0.891
The Genome Aggregation DatabaseAmericanSub838A=0.170G=0.830
The Genome Aggregation DatabaseEast AsianSub1620A=0.025G=0.975
The Genome Aggregation DatabaseEuropeSub18454A=0.142G=0.857
The Genome Aggregation DatabaseGlobalStudy-wide29936A=0.127G=0.872
The Genome Aggregation DatabaseOtherSub302A=0.100G=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.129G=0.870
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.189G=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
rs22624250.000135alcohol consumption23743675

eQTL of rs2262425 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238984129SCLYENSG00000132330.12A>G7.8532e-1014599Cerebellum
Chr2:238984129SCLYENSG00000132330.12A>G2.8719e-414599Frontal_Cortex_BA9
Chr2:238984129SCLYENSG00000132330.12A>G1.0714e-814599Cortex
Chr2:238984129SCLYENSG00000132330.12A>G2.0850e-814599Cerebellar_Hemisphere
Chr2:238984129SCLYENSG00000132330.12A>G1.4177e-314599Caudate_basal_ganglia
Chr2:238984129SCLYENSG00000132330.12A>G7.2091e-414599Anterior_cingulate_cortex

meQTL of rs2262425 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 )
chr2238950342238950447E067-33682
chr2238951505238951913E067-32216
chr2238970839238970899E067-13230
chr2238990205238990255E0676076
chr2238990452238990751E0676323
chr2238970839238970899E068-13230
chr2239017313239017876E06833184
chr2238951505238951913E069-32216
chr2238970839238970899E069-13230
chr2238989790238989866E0695661
chr2238989941238990032E0695812
chr2238990205238990255E0696076
chr2238970839238970899E070-13230
chr2238950342238950447E071-33682
chr2238951505238951913E071-32216
chr2238951961238952020E071-32109
chr2238970839238970899E071-13230
chr2238989247238989354E0715118
chr2238989790238989866E0715661
chr2238989941238990032E0715812
chr2238990205238990255E0716076
chr2238990452238990751E0716323
chr2239007116239007529E07122987
chr2239017176239017226E07133047
chr2239017313239017876E07133184
chr2238950342238950447E072-33682
chr2238989790238989866E0725661
chr2238989941238990032E0725812
chr2238990205238990255E0726076
chr2238990452238990751E0726323
chr2239014417239014467E07230288
chr2239014951239015001E07230822
chr2238970839238970899E073-13230
chr2239014951239015001E07330822
chr2238950342238950447E074-33682
chr2238951505238951913E074-32216
chr2238989790238989866E0745661
chr2238989941238990032E0745812
chr2238990452238990751E0746323
chr2239017313239017876E07433184
chr2238994008238994058E0819879
chr2238994372238994803E08110243
chr2238993565238993671E0829436
chr2238994008238994058E0829879










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-13522
chr2238968700238970607E068-13522
chr2238968700238970607E069-13522
chr2238968700238970607E070-13522
chr2238968700238970607E071-13522
chr2238968700238970607E072-13522
chr2238968700238970607E073-13522
chr2238968700238970607E074-13522
chr2238968700238970607E081-13522
chr2238968700238970607E082-13522