rs821482

Homo sapiens
T>C
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0138 (4111/29594,GnomAD)
T==0148 (4334/29118,TOPMED)
T==0165 (824/5008,1000G)
T==0177 (681/3854,ALSPAC)
T==0189 (702/3708,TWINSUK)
chr2:238062470 (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.238062470T>C
GRCh37.p13 chr 2NC_000002.11:g.238971111T>C

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
1000GenomesAfricanSub1322T=0.151C=0.849
1000GenomesAmericanSub694T=0.180C=0.820
1000GenomesEast AsianSub1008T=0.029C=0.971
1000GenomesEuropeSub1006T=0.163C=0.837
1000GenomesGlobalStudy-wide5008T=0.165C=0.835
1000GenomesSouth AsianSub978T=0.310C=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.177C=0.823
The Genome Aggregation DatabaseAfricanSub8638T=0.148C=0.852
The Genome Aggregation DatabaseAmericanSub828T=0.180C=0.820
The Genome Aggregation DatabaseEast AsianSub1612T=0.026C=0.974
The Genome Aggregation DatabaseEuropeSub18214T=0.143C=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29594T=0.138C=0.861
The Genome Aggregation DatabaseOtherSub302T=0.100C=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.148C=0.851
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.189C=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
rs8214826.22E-05alcohol consumption23743675

eQTL of rs821482 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238971111SCLYENSG00000132330.12T>C7.8532e-101581Cerebellum
Chr2:238971111SCLYENSG00000132330.12T>C1.0714e-81581Cortex
Chr2:238971111SCLYENSG00000132330.12T>C2.0850e-81581Cerebellar_Hemisphere
Chr2:238971111SCLYENSG00000132330.12T>C1.4177e-31581Caudate_basal_ganglia
Chr2:238971111SCLYENSG00000132330.12T>C7.2091e-41581Anterior_cingulate_cortex

meQTL of rs821482 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 )
chr2238931681238931768E067-39343
chr2238950342238950447E067-20664
chr2238951505238951913E067-19198
chr2238970839238970899E067-212
chr2238990205238990255E06719094
chr2238990452238990751E06719341
chr2238970839238970899E068-212
chr2239017313239017876E06846202
chr2238928552238929028E069-42083
chr2238951505238951913E069-19198
chr2238970839238970899E069-212
chr2238989790238989866E06918679
chr2238989941238990032E06918830
chr2238990205238990255E06919094
chr2238970839238970899E070-212
chr2238950342238950447E071-20664
chr2238951505238951913E071-19198
chr2238951961238952020E071-19091
chr2238970839238970899E071-212
chr2238989247238989354E07118136
chr2238989790238989866E07118679
chr2238989941238990032E07118830
chr2238990205238990255E07119094
chr2238990452238990751E07119341
chr2239007116239007529E07136005
chr2239017176239017226E07146065
chr2239017313239017876E07146202
chr2238950342238950447E072-20664
chr2238989790238989866E07218679
chr2238989941238990032E07218830
chr2238990205238990255E07219094
chr2238990452238990751E07219341
chr2239014417239014467E07243306
chr2239014951239015001E07243840
chr2238970839238970899E073-212
chr2239014951239015001E07343840
chr2238931681238931768E074-39343
chr2238950342238950447E074-20664
chr2238951505238951913E074-19198
chr2238989790238989866E07418679
chr2238989941238990032E07418830
chr2238990452238990751E07419341
chr2239017313239017876E07446202
chr2238994008238994058E08122897
chr2238994372238994803E08123261
chr2238993565238993671E08222454
chr2238994008238994058E08222897










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-504
chr2238968700238970607E068-504
chr2238968700238970607E069-504
chr2238968700238970607E070-504
chr2238968700238970607E071-504
chr2238968700238970607E072-504
chr2238968700238970607E073-504
chr2238968700238970607E074-504
chr2238968700238970607E081-504
chr2238968700238970607E082-504