rs865380

Homo sapiens
C>G
UBE2F-SCLY : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0138 (4138/29824,GnomAD)
G=0148 (4325/29118,TOPMED)
G=0164 (821/5008,1000G)
G=0176 (679/3854,ALSPAC)
G=0189 (702/3708,TWINSUK)
chr2:238055357 (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.238055357C>G
GRCh37.p13 chr 2NC_000002.11:g.238963998C>G

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=0.852G=0.148
1000GenomesAmericanSub694C=0.820G=0.180
1000GenomesEast AsianSub1008C=0.971G=0.029
1000GenomesEuropeSub1006C=0.835G=0.165
1000GenomesGlobalStudy-wide5008C=0.836G=0.164
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 DatabaseAfricanSub8700C=0.854G=0.146
The Genome Aggregation DatabaseAmericanSub836C=0.820G=0.180
The Genome Aggregation DatabaseEast AsianSub1616C=0.975G=0.025
The Genome Aggregation DatabaseEuropeSub18370C=0.856G=0.143
The Genome Aggregation DatabaseGlobalStudy-wide29824C=0.861G=0.138
The Genome Aggregation DatabaseOtherSub302C=0.890G=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.851G=0.148
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
rs8653800.00011alcohol consumption23743675

eQTL of rs865380 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:238963998SCLYENSG00000132330.12C>G7.8532e-10-5532Cerebellum
Chr2:238963998SCLYENSG00000132330.12C>G1.0714e-8-5532Cortex
Chr2:238963998SCLYENSG00000132330.12C>G2.0850e-8-5532Cerebellar_Hemisphere
Chr2:238963998SCLYENSG00000132330.12C>G1.4177e-3-5532Caudate_basal_ganglia
Chr2:238963998SCLYENSG00000132330.12C>G7.2091e-4-5532Anterior_cingulate_cortex

meQTL of rs865380 in Fetal Brain

Probe ID Position Gene beta p-value
cg03558837chr2:239029375ESPNL0.05953135628673041.2684e-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 )
chr2238917607238917771E067-46227
chr2238931681238931768E067-32230
chr2238950342238950447E067-13551
chr2238951505238951913E067-12085
chr2238970839238970899E0676841
chr2238990205238990255E06726207
chr2238990452238990751E06726454
chr2238970839238970899E0686841
chr2238918301238918438E069-45560
chr2238919370238919610E069-44388
chr2238919757238919867E069-44131
chr2238928552238929028E069-34970
chr2238951505238951913E069-12085
chr2238970839238970899E0696841
chr2238989790238989866E06925792
chr2238989941238990032E06925943
chr2238990205238990255E06926207
chr2238970839238970899E0706841
chr2238917607238917771E071-46227
chr2238917904238917968E071-46030
chr2238918301238918438E071-45560
chr2238919370238919610E071-44388
chr2238919757238919867E071-44131
chr2238950342238950447E071-13551
chr2238951505238951913E071-12085
chr2238951961238952020E071-11978
chr2238970839238970899E0716841
chr2238989247238989354E07125249
chr2238989790238989866E07125792
chr2238989941238990032E07125943
chr2238990205238990255E07126207
chr2238990452238990751E07126454
chr2239007116239007529E07143118
chr2238917607238917771E072-46227
chr2238950342238950447E072-13551
chr2238989790238989866E07225792
chr2238989941238990032E07225943
chr2238990205238990255E07226207
chr2238990452238990751E07226454
chr2238970839238970899E0736841
chr2238915164238915422E074-48576
chr2238917607238917771E074-46227
chr2238917904238917968E074-46030
chr2238918301238918438E074-45560
chr2238919370238919610E074-44388
chr2238919757238919867E074-44131
chr2238931681238931768E074-32230
chr2238950342238950447E074-13551
chr2238951505238951913E074-12085
chr2238989790238989866E07425792
chr2238989941238990032E07425943
chr2238990452238990751E07426454
chr2238994008238994058E08130010
chr2238994372238994803E08130374
chr2238993565238993671E08229567
chr2238994008238994058E08230010










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2238968700238970607E0674702
chr2238968700238970607E0684702
chr2238968700238970607E0694702
chr2238968700238970607E0704702
chr2238968700238970607E0714702
chr2238968700238970607E0724702
chr2238968700238970607E0734702
chr2238968700238970607E0744702
chr2238968700238970607E0814702
chr2238968700238970607E0824702