rs2243545

Homo sapiens
C>T
UBE2F-SCLY : Intron Variant
SCLY : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0179 (5340/29810,GnomAD)
C==0211 (6143/29118,TOPMED)
C==0205 (1026/5008,1000G)
C==0176 (680/3854,ALSPAC)
C==0189 (701/3708,TWINSUK)
chr2:238060509 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
53 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238060509C>T
GRCh37.p13 chr 2NC_000002.11:g.238969150C>T

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=0.299T=0.701
1000GenomesAmericanSub694C=0.190T=0.810
1000GenomesEast AsianSub1008C=0.029T=0.971
1000GenomesEuropeSub1006C=0.163T=0.837
1000GenomesGlobalStudy-wide5008C=0.205T=0.795
1000GenomesSouth AsianSub978C=0.310T=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.176T=0.824
The Genome Aggregation DatabaseAfricanSub8660C=0.286T=0.714
The Genome Aggregation DatabaseAmericanSub836C=0.180T=0.820
The Genome Aggregation DatabaseEast AsianSub1622C=0.025T=0.975
The Genome Aggregation DatabaseEuropeSub18390C=0.143T=0.856
The Genome Aggregation DatabaseGlobalStudy-wide29810C=0.179T=0.820
The Genome Aggregation DatabaseOtherSub302C=0.100T=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.211T=0.789
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.189T=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
rs22435456.15E-05alcohol consumption23743675

eQTL of rs2243545 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238969150SCLYENSG00000132330.12C>T7.8532e-10-380Cerebellum
Chr2:238969150SCLYENSG00000132330.12C>T1.0714e-8-380Cortex
Chr2:238969150SCLYENSG00000132330.12C>T2.0850e-8-380Cerebellar_Hemisphere
Chr2:238969150SCLYENSG00000132330.12C>T1.4177e-3-380Caudate_basal_ganglia
Chr2:238969150SCLYENSG00000132330.12C>T7.2091e-4-380Anterior_cingulate_cortex

meQTL of rs2243545 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 )
chr2238931681238931768E067-37382
chr2238950342238950447E067-18703
chr2238951505238951913E067-17237
chr2238970839238970899E0671689
chr2238990205238990255E06721055
chr2238990452238990751E06721302
chr2238970839238970899E0681689
chr2239017313239017876E06848163
chr2238919370238919610E069-49540
chr2238919757238919867E069-49283
chr2238928552238929028E069-40122
chr2238951505238951913E069-17237
chr2238970839238970899E0691689
chr2238989790238989866E06920640
chr2238989941238990032E06920791
chr2238990205238990255E06921055
chr2238970839238970899E0701689
chr2238919370238919610E071-49540
chr2238919757238919867E071-49283
chr2238950342238950447E071-18703
chr2238951505238951913E071-17237
chr2238951961238952020E071-17130
chr2238970839238970899E0711689
chr2238989247238989354E07120097
chr2238989790238989866E07120640
chr2238989941238990032E07120791
chr2238990205238990255E07121055
chr2238990452238990751E07121302
chr2239007116239007529E07137966
chr2239017176239017226E07148026
chr2239017313239017876E07148163
chr2238950342238950447E072-18703
chr2238989790238989866E07220640
chr2238989941238990032E07220791
chr2238990205238990255E07221055
chr2238990452238990751E07221302
chr2239014417239014467E07245267
chr2239014951239015001E07245801
chr2238970839238970899E0731689
chr2239014951239015001E07345801
chr2238919370238919610E074-49540
chr2238919757238919867E074-49283
chr2238931681238931768E074-37382
chr2238950342238950447E074-18703
chr2238951505238951913E074-17237
chr2238989790238989866E07420640
chr2238989941238990032E07420791
chr2238990452238990751E07421302
chr2239017313239017876E07448163
chr2238994008238994058E08124858
chr2238994372238994803E08125222
chr2238993565238993671E08224415
chr2238994008238994058E08224858










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E0670
chr2238968700238970607E0680
chr2238968700238970607E0690
chr2238968700238970607E0700
chr2238968700238970607E0710
chr2238968700238970607E0720
chr2238968700238970607E0730
chr2238968700238970607E0740
chr2238968700238970607E0810
chr2238968700238970607E0820