rs2278742

Homo sapiens
C>T
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0451 (44816/99354,ExAC)
C==0456 (13644/29866,GnomAD)
C==0465 (13563/29118,TOPMED)
C==0497 (2488/5008,1000G)
C==0478 (1842/3854,ALSPAC)
C==0493 (1827/3708,TWINSUK)
chr2:238083155 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
44 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238083155C>T
GRCh37.p13 chr 2NC_000002.11:g.238991796C>T

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
1000GenomesAfricanSub1322C=0.430T=0.570
1000GenomesAmericanSub694C=0.440T=0.560
1000GenomesEast AsianSub1008C=0.514T=0.486
1000GenomesEuropeSub1006C=0.450T=0.550
1000GenomesGlobalStudy-wide5008C=0.497T=0.503
1000GenomesSouth AsianSub978C=0.660T=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.478T=0.522
The Exome Aggregation ConsortiumAmericanSub17352C=0.423T=0.576
The Exome Aggregation ConsortiumAsianSub20588C=0.582T=0.418
The Exome Aggregation ConsortiumEuropeSub60636C=0.414T=0.585
The Exome Aggregation ConsortiumGlobalStudy-wide99354C=0.451T=0.548
The Exome Aggregation ConsortiumOtherSub778C=0.440T=0.560
The Genome Aggregation DatabaseAfricanSub8696C=0.432T=0.568
The Genome Aggregation DatabaseAmericanSub834C=0.520T=0.480
The Genome Aggregation DatabaseEast AsianSub1614C=0.563T=0.437
The Genome Aggregation DatabaseEuropeSub18420C=0.456T=0.543
The Genome Aggregation DatabaseGlobalStudy-wide29866C=0.456T=0.543
The Genome Aggregation DatabaseOtherSub302C=0.450T=0.550
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.465T=0.534
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.493T=0.507
PMID Title Author Journal
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs22787428.01E-05alcohol consumption23953852

eQTL of rs2278742 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs2278742 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

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 )
chr2238950342238950447E067-41349
chr2238951505238951913E067-39883
chr2238970839238970899E067-20897
chr2238990205238990255E067-1541
chr2238990452238990751E067-1045
chr2238970839238970899E068-20897
chr2239017313239017876E06825517
chr2238951505238951913E069-39883
chr2238970839238970899E069-20897
chr2238989790238989866E069-1930
chr2238989941238990032E069-1764
chr2238990205238990255E069-1541
chr2238970839238970899E070-20897
chr2238950342238950447E071-41349
chr2238951505238951913E071-39883
chr2238951961238952020E071-39776
chr2238970839238970899E071-20897
chr2238989247238989354E071-2442
chr2238989790238989866E071-1930
chr2238989941238990032E071-1764
chr2238990205238990255E071-1541
chr2238990452238990751E071-1045
chr2239007116239007529E07115320
chr2239017176239017226E07125380
chr2239017313239017876E07125517
chr2238950342238950447E072-41349
chr2238989790238989866E072-1930
chr2238989941238990032E072-1764
chr2238990205238990255E072-1541
chr2238990452238990751E072-1045
chr2239014417239014467E07222621
chr2239014951239015001E07223155
chr2238970839238970899E073-20897
chr2239014951239015001E07323155
chr2238950342238950447E074-41349
chr2238951505238951913E074-39883
chr2238989790238989866E074-1930
chr2238989941238990032E074-1764
chr2238990452238990751E074-1045
chr2239017313239017876E07425517
chr2238994008238994058E0812212
chr2238994372238994803E0812576
chr2238993565238993671E0821769
chr2238994008238994058E0822212










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-21189
chr2238968700238970607E068-21189
chr2238968700238970607E069-21189
chr2238968700238970607E070-21189
chr2238968700238970607E071-21189
chr2238968700238970607E072-21189
chr2238968700238970607E073-21189
chr2238968700238970607E074-21189
chr2238968700238970607E081-21189
chr2238968700238970607E082-21189