rs1054078

Homo sapiens
A>G
SNX16 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0331 (9885/29842,GnomAD)
A==0339 (9894/29118,TOPMED)
A==0381 (1910/5008,1000G)
A==0332 (1279/3854,ALSPAC)
A==0320 (1188/3708,TWINSUK)
chr8:81799918 (GRCh38.p7) (8q21.13)
AD
GWASdb2
1   publication(s)
See rs on genome
93 Enhancers around
39 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.81799918A>G
GRCh37.p13 chr 8NC_000008.10:g.82712153A>G

Gene: SNX16, sorting nexin 16(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SNX16 transcript variant 3NM_152837.2:c.N/A3 Prime UTR Variant
SNX16 transcript variant 2NM_152836.2:c.N/A3 Prime UTR Variant
SNX16 transcript variant 1NM_022133.3:c.N/A3 Prime UTR Variant
SNX16 transcript variant X2XM_005251283.2:c.N/A3 Prime UTR Variant
SNX16 transcript variant X1XM_005251282.4:c.N/A3 Prime UTR Variant
SNX16 transcript variant X3XM_011517574.2:c.N/A3 Prime UTR Variant
SNX16 transcript variant X3XR_001745572.1:n.N/AGenic Downstream Transcript Variant
SNX16 transcript variant X5XR_001745573.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.321G=0.679
1000GenomesAmericanSub694A=0.390G=0.610
1000GenomesEast AsianSub1008A=0.597G=0.403
1000GenomesEuropeSub1006A=0.327G=0.673
1000GenomesGlobalStudy-wide5008A=0.381G=0.619
1000GenomesSouth AsianSub978A=0.290G=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.332G=0.668
The Genome Aggregation DatabaseAfricanSub8692A=0.327G=0.673
The Genome Aggregation DatabaseAmericanSub834A=0.320G=0.680
The Genome Aggregation DatabaseEast AsianSub1616A=0.631G=0.369
The Genome Aggregation DatabaseEuropeSub18398A=0.307G=0.693
The Genome Aggregation DatabaseGlobalStudy-wide29842A=0.331G=0.668
The Genome Aggregation DatabaseOtherSub302A=0.370G=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.339G=0.660
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.320G=0.680
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
rs10540783.02E-05alcohol consumption23743675

eQTL of rs1054078 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 rs1054078 in Fetal Brain

Probe ID Position Gene beta p-value
cg17211192chr8:82754475SNX160.06479748977329936.7363e-27
cg27398817chr8:82754497SNX160.03840175693116452.7176e-15
cg23324259chr8:82754387SNX160.01771319224007824.3004e-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 )
chr88272692182727044E06714768
chr88272708482727145E06714931
chr88272739782727713E06715244
chr88275141582751459E06739262
chr88275155182751632E06739398
chr88275169382751743E06739540
chr88275176982751905E06739616
chr88275192082751978E06739767
chr88275205182752101E06739898
chr88275213682752286E06739983
chr88275242482752500E06740271
chr88275252382752586E06740370
chr88274913582749745E06836982
chr88275040382750493E06838250
chr88275055782750622E06838404
chr88275073382750913E06838580
chr88275118682751259E06839033
chr88275141582751459E06839262
chr88275155182751632E06839398
chr88275169382751743E06839540
chr88275242482752500E06840271
chr88275252382752586E06840370
chr88275264882752702E06840495
chr88275205182752101E06939898
chr88275213682752286E06939983
chr88275242482752500E06940271
chr88275252382752586E06940370
chr88275264882752702E06940495
chr88270876682709232E070-2921
chr88270927582709325E070-2828
chr88270935482709440E070-2713
chr88273635982736422E07024206
chr88273760682737656E07025453
chr88273770482737783E07025551
chr88274913582749745E07036982
chr88272692182727044E07114768
chr88272739782727713E07115244
chr88275040382750493E07138250
chr88275055782750622E07138404
chr88275073382750913E07138580
chr88275176982751905E07139616
chr88275192082751978E07139767
chr88275205182752101E07139898
chr88275213682752286E07139983
chr88275242482752500E07140271
chr88275252382752586E07140370
chr88275264882752702E07140495
chr88269268482693377E072-18776
chr88272629482726439E07214141
chr88272692182727044E07214768
chr88272708482727145E07214931
chr88272739782727713E07215244
chr88272739782727713E07315244
chr88272692182727044E07414768
chr88275040382750493E07438250
chr88275055782750622E07438404
chr88275073382750913E07438580
chr88275118682751259E07439033
chr88275141582751459E07439262
chr88275155182751632E07439398
chr88275169382751743E07439540
chr88275176982751905E07439616
chr88275192082751978E07439767
chr88275205182752101E07439898
chr88275213682752286E07439983
chr88275242482752500E07440271
chr88275252382752586E07440370
chr88275264882752702E07440495
chr88269268482693377E081-18776
chr88274894182748991E08136788
chr88275118682751259E08139033
chr88275141582751459E08139262
chr88275155182751632E08139398
chr88275169382751743E08139540
chr88275176982751905E08139616
chr88275192082751978E08139767
chr88275205182752101E08139898
chr88275213682752286E08139983
chr88275242482752500E08140271
chr88275252382752586E08140370
chr88275264882752702E08140495
chr88269939382699447E082-12706
chr88269957982699654E082-12499
chr88274913582749745E08236982
chr88274982582749873E08237672
chr88275155182751632E08239398
chr88275169382751743E08239540
chr88275176982751905E08239616
chr88275192082751978E08239767
chr88275205182752101E08239898
chr88275213682752286E08239983
chr88275242482752500E08240271
chr88275252382752586E08240370










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr88275290282753069E06740749
chr88275314082753307E06740987
chr88275349982753591E06741346
chr88275360282754599E06741449
chr88275349982753591E06841346
chr88275360282754599E06841449
chr88275461982755486E06842466
chr88275290282753069E06940749
chr88275314082753307E06940987
chr88275349982753591E06941346
chr88275360282754599E06941449
chr88275290282753069E07040749
chr88275314082753307E07040987
chr88275349982753591E07041346
chr88275360282754599E07041449
chr88275290282753069E07140749
chr88275314082753307E07140987
chr88275349982753591E07141346
chr88275360282754599E07141449
chr88275461982755486E07142466
chr88275290282753069E07240749
chr88275314082753307E07240987
chr88275349982753591E07241346
chr88275360282754599E07241449
chr88275290282753069E07340749
chr88275314082753307E07340987
chr88275349982753591E07341346
chr88275360282754599E07341449
chr88275461982755486E07342466
chr88275314082753307E07440987
chr88275349982753591E07441346
chr88275360282754599E07441449
chr88275461982755486E07442466
chr88275360282754599E08141449
chr88275290282753069E08240749
chr88275314082753307E08240987
chr88275349982753591E08241346
chr88275360282754599E08241449
chr88275461982755486E08242466