rs821480

Homo sapiens
T>C
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0127 (3833/29986,GnomAD)
T==0131 (3815/29118,TOPMED)
T==0149 (748/5008,1000G)
T==0175 (676/3854,ALSPAC)
T==0189 (700/3708,TWINSUK)
chr2:238064186 (GRCh38.p7) (2q37.3)
AD
GWASdb2
2   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.238064186T>C
GRCh37.p13 chr 2NC_000002.11:g.238972827T>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=0.094C=0.906
1000GenomesAmericanSub694T=0.180C=0.820
1000GenomesEast AsianSub1008T=0.029C=0.971
1000GenomesEuropeSub1006T=0.163C=0.837
1000GenomesGlobalStudy-wide5008T=0.149C=0.851
1000GenomesSouth AsianSub978T=0.310C=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.175C=0.825
The Genome Aggregation DatabaseAfricanSub8716T=0.110C=0.890
The Genome Aggregation DatabaseAmericanSub838T=0.180C=0.820
The Genome Aggregation DatabaseEast AsianSub1620T=0.025C=0.975
The Genome Aggregation DatabaseEuropeSub18510T=0.143C=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29986T=0.127C=0.872
The Genome Aggregation DatabaseOtherSub302T=0.100C=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.131C=0.869
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.189C=0.811
PMID Title Author Journal
23285077Polymorphisms in the non-muscle myosin heavy chain gene (MYH9) are associated with lower glomerular filtration rate in mixed ancestry diabetic subjects from South Africa.Matsha TEPLoS One
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
rs8214807.43E-05alcohol consumption23743675

eQTL of rs821480 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238972827SCLYENSG00000132330.12T>C7.8532e-103297Cerebellum
Chr2:238972827SCLYENSG00000132330.12T>C1.0714e-83297Cortex
Chr2:238972827SCLYENSG00000132330.12T>C2.0850e-83297Cerebellar_Hemisphere
Chr2:238972827SCLYENSG00000132330.12T>C1.4177e-33297Caudate_basal_ganglia
Chr2:238972827SCLYENSG00000132330.12T>C7.2091e-43297Anterior_cingulate_cortex

meQTL of rs821480 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.06710898536011691.7235e-15

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 )
chr2238931681238931768E067-41059
chr2238950342238950447E067-22380
chr2238951505238951913E067-20914
chr2238970839238970899E067-1928
chr2238990205238990255E06717378
chr2238990452238990751E06717625
chr2238970839238970899E068-1928
chr2239017313239017876E06844486
chr2238928552238929028E069-43799
chr2238951505238951913E069-20914
chr2238970839238970899E069-1928
chr2238989790238989866E06916963
chr2238989941238990032E06917114
chr2238990205238990255E06917378
chr2238970839238970899E070-1928
chr2238950342238950447E071-22380
chr2238951505238951913E071-20914
chr2238951961238952020E071-20807
chr2238970839238970899E071-1928
chr2238989247238989354E07116420
chr2238989790238989866E07116963
chr2238989941238990032E07117114
chr2238990205238990255E07117378
chr2238990452238990751E07117625
chr2239007116239007529E07134289
chr2239017176239017226E07144349
chr2239017313239017876E07144486
chr2238950342238950447E072-22380
chr2238989790238989866E07216963
chr2238989941238990032E07217114
chr2238990205238990255E07217378
chr2238990452238990751E07217625
chr2239014417239014467E07241590
chr2239014951239015001E07242124
chr2238970839238970899E073-1928
chr2239014951239015001E07342124
chr2238931681238931768E074-41059
chr2238950342238950447E074-22380
chr2238951505238951913E074-20914
chr2238989790238989866E07416963
chr2238989941238990032E07417114
chr2238990452238990751E07417625
chr2239017313239017876E07444486
chr2238994008238994058E08121181
chr2238994372238994803E08121545
chr2238993565238993671E08220738
chr2238994008238994058E08221181










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-2220
chr2238968700238970607E068-2220
chr2238968700238970607E069-2220
chr2238968700238970607E070-2220
chr2238968700238970607E071-2220
chr2238968700238970607E072-2220
chr2238968700238970607E073-2220
chr2238968700238970607E074-2220
chr2238968700238970607E081-2220
chr2238968700238970607E082-2220