rs13006807

Homo sapiens
C>T
ESPNL : 2KB Upstream Variant
SCLY : 500B Downstream Variant
UBE2F-SCLY : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0126 (3774/29934,GnomAD)
T=0130 (3793/29118,TOPMED)
T=0149 (746/5008,1000G)
T=0178 (686/3854,ALSPAC)
T=0189 (699/3708,TWINSUK)
chr2:238099901 (GRCh38.p7) (2q37.3)
AD
GWASdb2
1   publication(s)
See rs on genome
35 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.238099901C>T
GRCh37.p13 chr 2NC_000002.11:g.239008542C>T

Gene: SCLY, selenocysteine lyase(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
SCLY transcriptNM_016510.5:c.N/ADownstream Transcript Variant

Gene: ESPNL, espin-like(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
ESPNL transcript variant 1NM_194312.3:c.N/AUpstream Transcript Variant
ESPNL transcript variant 2NM_001308370.1:c.N/AN/A
ESPNL transcript variant X1XM_011511087.1:c.N/AN/A

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
UBE2F-SCLY transcriptNR_037904.1:n.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.908T=0.092
1000GenomesAmericanSub694C=0.820T=0.180
1000GenomesEast AsianSub1008C=0.971T=0.029
1000GenomesEuropeSub1006C=0.838T=0.162
1000GenomesGlobalStudy-wide5008C=0.851T=0.149
1000GenomesSouth AsianSub978C=0.690T=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.822T=0.178
The Genome Aggregation DatabaseAfricanSub8714C=0.894T=0.106
The Genome Aggregation DatabaseAmericanSub836C=0.830T=0.170
The Genome Aggregation DatabaseEast AsianSub1620C=0.976T=0.024
The Genome Aggregation DatabaseEuropeSub18462C=0.857T=0.142
The Genome Aggregation DatabaseGlobalStudy-wide29934C=0.873T=0.126
The Genome Aggregation DatabaseOtherSub302C=0.890T=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.869T=0.130
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.811T=0.189
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
rs130068070.000131alcohol consumption23743675

eQTL of rs13006807 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:239008542SCLYENSG00000132330.12C>T7.8532e-1039012Cerebellum
Chr2:239008542SCLYENSG00000132330.12C>T1.0714e-839012Cortex
Chr2:239008542SCLYENSG00000132330.12C>T2.0850e-839012Cerebellar_Hemisphere
Chr2:239008542SCLYENSG00000132330.12C>T1.4177e-339012Caudate_basal_ganglia
Chr2:239008542SCLYENSG00000132330.12C>T7.2091e-439012Anterior_cingulate_cortex

meQTL of rs13006807 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.06453557400157633.5581e-14

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 )
chr2238970839238970899E067-37643
chr2238990205238990255E067-18287
chr2238990452238990751E067-17791
chr2238970839238970899E068-37643
chr2239017313239017876E0688771
chr2238970839238970899E069-37643
chr2238989790238989866E069-18676
chr2238989941238990032E069-18510
chr2238990205238990255E069-18287
chr2238970839238970899E070-37643
chr2238970839238970899E071-37643
chr2238989247238989354E071-19188
chr2238989790238989866E071-18676
chr2238989941238990032E071-18510
chr2238990205238990255E071-18287
chr2238990452238990751E071-17791
chr2239007116239007529E071-1013
chr2239017176239017226E0718634
chr2239017313239017876E0718771
chr2238989790238989866E072-18676
chr2238989941238990032E072-18510
chr2238990205238990255E072-18287
chr2238990452238990751E072-17791
chr2239014417239014467E0725875
chr2239014951239015001E0726409
chr2238970839238970899E073-37643
chr2239014951239015001E0736409
chr2238989790238989866E074-18676
chr2238989941238990032E074-18510
chr2238990452238990751E074-17791
chr2239017313239017876E0748771
chr2238994008238994058E081-14484
chr2238994372238994803E081-13739
chr2238993565238993671E082-14871
chr2238994008238994058E082-14484










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-37935
chr2238968700238970607E068-37935
chr2238968700238970607E069-37935
chr2238968700238970607E070-37935
chr2238968700238970607E071-37935
chr2238968700238970607E072-37935
chr2238968700238970607E073-37935
chr2238968700238970607E074-37935
chr2238968700238970607E081-37935
chr2238968700238970607E082-37935