rs7591078

Homo sapiens
C>G
SCLY : Intron Variant
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0126 (3799/29958,GnomAD)
G=0131 (3833/29118,TOPMED)
G=0148 (743/5008,1000G)
G=0176 (679/3854,ALSPAC)
G=0189 (699/3708,TWINSUK)
chr2:238096373 (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.238096373C>G
GRCh37.p13 chr 2NC_000002.11:g.239005014C>G

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=0.909G=0.091
1000GenomesAmericanSub694C=0.820G=0.180
1000GenomesEast AsianSub1008C=0.971G=0.029
1000GenomesEuropeSub1006C=0.838G=0.162
1000GenomesGlobalStudy-wide5008C=0.852G=0.148
1000GenomesSouth AsianSub978C=0.690G=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.824G=0.176
The Genome Aggregation DatabaseAfricanSub8724C=0.892G=0.108
The Genome Aggregation DatabaseAmericanSub838C=0.830G=0.170
The Genome Aggregation DatabaseEast AsianSub1620C=0.975G=0.025
The Genome Aggregation DatabaseEuropeSub18474C=0.857G=0.142
The Genome Aggregation DatabaseGlobalStudy-wide29958C=0.873G=0.126
The Genome Aggregation DatabaseOtherSub302C=0.890G=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.868G=0.131
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.811G=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
rs75910780.000106alcohol consumption23743675

eQTL of rs7591078 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:239005014SCLYENSG00000132330.12C>G7.8532e-1035484Cerebellum
Chr2:239005014SCLYENSG00000132330.12C>G2.8719e-435484Frontal_Cortex_BA9
Chr2:239005014SCLYENSG00000132330.12C>G1.0714e-835484Cortex
Chr2:239005014SCLYENSG00000132330.12C>G2.0850e-835484Cerebellar_Hemisphere
Chr2:239005014SCLYENSG00000132330.12C>G1.4177e-335484Caudate_basal_ganglia
Chr2:239005014SCLYENSG00000132330.12C>G7.2091e-435484Anterior_cingulate_cortex

meQTL of rs7591078 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.06462263479058882.4442e-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 )
chr2238970839238970899E067-34115
chr2238990205238990255E067-14759
chr2238990452238990751E067-14263
chr2238970839238970899E068-34115
chr2239017313239017876E06812299
chr2238970839238970899E069-34115
chr2238989790238989866E069-15148
chr2238989941238990032E069-14982
chr2238990205238990255E069-14759
chr2238970839238970899E070-34115
chr2238970839238970899E071-34115
chr2238989247238989354E071-15660
chr2238989790238989866E071-15148
chr2238989941238990032E071-14982
chr2238990205238990255E071-14759
chr2238990452238990751E071-14263
chr2239007116239007529E0712102
chr2239017176239017226E07112162
chr2239017313239017876E07112299
chr2238989790238989866E072-15148
chr2238989941238990032E072-14982
chr2238990205238990255E072-14759
chr2238990452238990751E072-14263
chr2239014417239014467E0729403
chr2239014951239015001E0729937
chr2238970839238970899E073-34115
chr2239014951239015001E0739937
chr2238989790238989866E074-15148
chr2238989941238990032E074-14982
chr2238990452238990751E074-14263
chr2239017313239017876E07412299
chr2238994008238994058E081-10956
chr2238994372238994803E081-10211
chr2238993565238993671E082-11343
chr2238994008238994058E082-10956










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E067-34407
chr2238968700238970607E068-34407
chr2238968700238970607E069-34407
chr2238968700238970607E070-34407
chr2238968700238970607E071-34407
chr2238968700238970607E072-34407
chr2238968700238970607E073-34407
chr2238968700238970607E074-34407
chr2238968700238970607E081-34407
chr2238968700238970607E082-34407