rs1374479

Homo sapiens
C>G
UBE2F-SCLY : Intron Variant
SCLY : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0179 (5384/29972,GnomAD)
C==0211 (6146/29118,TOPMED)
C==0205 (1026/5008,1000G)
C==0177 (681/3854,ALSPAC)
C==0189 (701/3708,TWINSUK)
chr2:238059384 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
56 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238059384C>G
GRCh37.p13 chr 2NC_000002.11:g.238968025C>G

Gene: SCLY, selenocysteine lyase(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
SCLY transcriptNM_016510.5:c.N/AUpstream Transcript 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=0.299G=0.701
1000GenomesAmericanSub694C=0.190G=0.810
1000GenomesEast AsianSub1008C=0.029G=0.971
1000GenomesEuropeSub1006C=0.163G=0.837
1000GenomesGlobalStudy-wide5008C=0.205G=0.795
1000GenomesSouth AsianSub978C=0.310G=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.177G=0.823
The Genome Aggregation DatabaseAfricanSub8722C=0.287G=0.713
The Genome Aggregation DatabaseAmericanSub838C=0.180G=0.820
The Genome Aggregation DatabaseEast AsianSub1620C=0.025G=0.975
The Genome Aggregation DatabaseEuropeSub18490C=0.143G=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29972C=0.179G=0.820
The Genome Aggregation DatabaseOtherSub302C=0.100G=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.211G=0.788
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=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
rs13744796.23E-05alcohol consumption23743675

eQTL of rs1374479 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238968025SCLYENSG00000132330.12C>G7.8532e-10-1505Cerebellum
Chr2:238968025SCLYENSG00000132330.12C>G1.0714e-8-1505Cortex
Chr2:238968025SCLYENSG00000132330.12C>G2.0850e-8-1505Cerebellar_Hemisphere
Chr2:238968025SCLYENSG00000132330.12C>G1.4177e-3-1505Caudate_basal_ganglia
Chr2:238968025SCLYENSG00000132330.12C>G7.2091e-4-1505Anterior_cingulate_cortex

meQTL of rs1374479 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.05528679478096757.5821e-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 )
chr2238931681238931768E067-36257
chr2238950342238950447E067-17578
chr2238951505238951913E067-16112
chr2238970839238970899E0672814
chr2238990205238990255E06722180
chr2238990452238990751E06722427
chr2238970839238970899E0682814
chr2239017313239017876E06849288
chr2238918301238918438E069-49587
chr2238919370238919610E069-48415
chr2238919757238919867E069-48158
chr2238928552238929028E069-38997
chr2238951505238951913E069-16112
chr2238970839238970899E0692814
chr2238989790238989866E06921765
chr2238989941238990032E06921916
chr2238990205238990255E06922180
chr2238970839238970899E0702814
chr2238918301238918438E071-49587
chr2238919370238919610E071-48415
chr2238919757238919867E071-48158
chr2238950342238950447E071-17578
chr2238951505238951913E071-16112
chr2238951961238952020E071-16005
chr2238970839238970899E0712814
chr2238989247238989354E07121222
chr2238989790238989866E07121765
chr2238989941238990032E07121916
chr2238990205238990255E07122180
chr2238990452238990751E07122427
chr2239007116239007529E07139091
chr2239017176239017226E07149151
chr2239017313239017876E07149288
chr2238950342238950447E072-17578
chr2238989790238989866E07221765
chr2238989941238990032E07221916
chr2238990205238990255E07222180
chr2238990452238990751E07222427
chr2239014417239014467E07246392
chr2239014951239015001E07246926
chr2238970839238970899E0732814
chr2239014951239015001E07346926
chr2238918301238918438E074-49587
chr2238919370238919610E074-48415
chr2238919757238919867E074-48158
chr2238931681238931768E074-36257
chr2238950342238950447E074-17578
chr2238951505238951913E074-16112
chr2238989790238989866E07421765
chr2238989941238990032E07421916
chr2238990452238990751E07422427
chr2239017313239017876E07449288
chr2238994008238994058E08125983
chr2238994372238994803E08126347
chr2238993565238993671E08225540
chr2238994008238994058E08225983










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067675
chr2238968700238970607E068675
chr2238968700238970607E069675
chr2238968700238970607E070675
chr2238968700238970607E071675
chr2238968700238970607E072675
chr2238968700238970607E073675
chr2238968700238970607E074675
chr2238968700238970607E081675
chr2238968700238970607E082675