rs13033964

Homo sapiens
G>A
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0128 (3838/29926,GnomAD)
A=0132 (3861/29118,TOPMED)
A=0149 (747/5008,1000G)
A=0177 (681/3854,ALSPAC)
A=0188 (697/3708,TWINSUK)
chr2:238096945 (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.238096945G>A
GRCh37.p13 chr 2NC_000002.11:g.239005586G>A

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
1000GenomesAfricanSub1322G=0.908A=0.092
1000GenomesAmericanSub694G=0.820A=0.180
1000GenomesEast AsianSub1008G=0.971A=0.029
1000GenomesEuropeSub1006G=0.838A=0.162
1000GenomesGlobalStudy-wide5008G=0.851A=0.149
1000GenomesSouth AsianSub978G=0.690A=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.823A=0.177
The Genome Aggregation DatabaseAfricanSub8704G=0.885A=0.115
The Genome Aggregation DatabaseAmericanSub838G=0.830A=0.170
The Genome Aggregation DatabaseEast AsianSub1622G=0.975A=0.025
The Genome Aggregation DatabaseEuropeSub18460G=0.858A=0.141
The Genome Aggregation DatabaseGlobalStudy-wide29926G=0.871A=0.128
The Genome Aggregation DatabaseOtherSub302G=0.890A=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.867A=0.132
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.812A=0.188
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
rs130339640.00011alcohol consumption23743675

eQTL of rs13033964 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:239005586SCLYENSG00000132330.12G>A7.8532e-1036056Cerebellum
Chr2:239005586SCLYENSG00000132330.12G>A2.8719e-436056Frontal_Cortex_BA9
Chr2:239005586SCLYENSG00000132330.12G>A1.0714e-836056Cortex
Chr2:239005586SCLYENSG00000132330.12G>A2.0850e-836056Cerebellar_Hemisphere
Chr2:239005586SCLYENSG00000132330.12G>A1.4177e-336056Caudate_basal_ganglia
Chr2:239005586SCLYENSG00000132330.12G>A7.2091e-436056Anterior_cingulate_cortex

meQTL of rs13033964 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 )
chr2238970839238970899E067-34687
chr2238990205238990255E067-15331
chr2238990452238990751E067-14835
chr2238970839238970899E068-34687
chr2239017313239017876E06811727
chr2238970839238970899E069-34687
chr2238989790238989866E069-15720
chr2238989941238990032E069-15554
chr2238990205238990255E069-15331
chr2238970839238970899E070-34687
chr2238970839238970899E071-34687
chr2238989247238989354E071-16232
chr2238989790238989866E071-15720
chr2238989941238990032E071-15554
chr2238990205238990255E071-15331
chr2238990452238990751E071-14835
chr2239007116239007529E0711530
chr2239017176239017226E07111590
chr2239017313239017876E07111727
chr2238989790238989866E072-15720
chr2238989941238990032E072-15554
chr2238990205238990255E072-15331
chr2238990452238990751E072-14835
chr2239014417239014467E0728831
chr2239014951239015001E0729365
chr2238970839238970899E073-34687
chr2239014951239015001E0739365
chr2238989790238989866E074-15720
chr2238989941238990032E074-15554
chr2238990452238990751E074-14835
chr2239017313239017876E07411727
chr2238994008238994058E081-11528
chr2238994372238994803E081-10783
chr2238993565238993671E082-11915
chr2238994008238994058E082-11528










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-34979
chr2238968700238970607E068-34979
chr2238968700238970607E069-34979
chr2238968700238970607E070-34979
chr2238968700238970607E071-34979
chr2238968700238970607E072-34979
chr2238968700238970607E073-34979
chr2238968700238970607E074-34979
chr2238968700238970607E081-34979
chr2238968700238970607E082-34979