rs13160562

Homo sapiens
G>A
ERAP1 : Intron Variant
LOC102724748 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0224 (6721/29942,GnomAD)
A=0203 (5911/29118,TOPMED)
A=0153 (767/5008,1000G)
A=0304 (1172/3854,ALSPAC)
A=0300 (1114/3708,TWINSUK)
chr5:96775667 (GRCh38.p7) (5q15)
AD
GWASdb2 | GWASCatalog
5   publication(s)
See rs on genome
70 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.96775667G>A
GRCh37.p13 chr 5NC_000005.9:g.96111371G>A
CAST RefSeqGeneNG_029490.1:g.118631G>A
ERAP1 RefSeqGeneNG_027839.1:g.43478C>T

Gene: ERAP1, endoplasmic reticulum aminopeptidase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ERAP1 transcript variant 1NM_016442.3:c.N/AIntron Variant
ERAP1 transcript variant 2NM_001040458.1:c.N/A3 Prime UTR Variant
ERAP1 transcript variant 3NM_001198541.1:c.N/A3 Prime UTR Variant
ERAP1 transcript variant X1XM_005272015.4:c.N/AIntron Variant
ERAP1 transcript variant X2XM_005272016.4:c.N/AIntron Variant
ERAP1 transcript variant X3XM_011543480.2:c.N/AIntron Variant
ERAP1 transcript variant X4XM_011543481.2:c.N/AIntron Variant
ERAP1 transcript variant X5XM_011543484.2:c.N/AIntron Variant
ERAP1 transcript variant X6XM_011543485.2:c.N/AIntron Variant
ERAP1 transcript variant X5XM_017009580.1:c.N/AIntron Variant
ERAP1 transcript variant X7XM_017009581.1:c.N/AIntron Variant
ERAP1 transcript variant X10XM_017009582.1:c.N/AIntron Variant
ERAP1 transcript variant X11XM_017009583.1:c.N/AIntron Variant
ERAP1 transcript variant X9XM_011543486.2:c.N/A3 Prime UTR Variant
ERAP1 transcript variant X12XR_001742119.1:n.N/AIntron Variant

Gene: LOC102724748, uncharacterized LOC102724748(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC102724748 transcript variant X1XR_001742445.1:n.N/AUpstream Transcript Variant
LOC102724748 transcript variant X2XR_001742446.1:n.N/AUpstream Transcript Variant
LOC102724748 transcript variant X3XR_427744.3:n.N/AUpstream Transcript Variant
LOC102724748 transcript variant X1XR_948592.2:n.N/AUpstream Transcript Variant
LOC102724748 transcript variant X5XR_948593.2:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.917A=0.083
1000GenomesAmericanSub694G=0.810A=0.190
1000GenomesEast AsianSub1008G=0.938A=0.062
1000GenomesEuropeSub1006G=0.673A=0.327
1000GenomesGlobalStudy-wide5008G=0.847A=0.153
1000GenomesSouth AsianSub978G=0.860A=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.696A=0.304
The Genome Aggregation DatabaseAfricanSub8724G=0.875A=0.125
The Genome Aggregation DatabaseAmericanSub838G=0.840A=0.160
The Genome Aggregation DatabaseEast AsianSub1622G=0.957A=0.043
The Genome Aggregation DatabaseEuropeSub18456G=0.710A=0.289
The Genome Aggregation DatabaseGlobalStudy-wide29942G=0.775A=0.224
The Genome Aggregation DatabaseOtherSub302G=0.740A=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.797A=0.203
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.700A=0.300
PMID Title Author Journal
23818875DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.Zhernakova DVPLoS Genet
19581569Genome-wide association study of alcohol dependence.Treutlein JArch Gen Psychiatry
22865700Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus.Greenawalt DMAm J Epidemiol
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A
21424381Identification of QTL genes for BMD variation using both linkage and gene-based association approaches.Li GHHum Genet

P-Value

SNP ID p-value Traits Study
rs131605627E-06alcohol dependence19581569

eQTL of rs13160562 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr5:96111371ERAP1ENSG00000164307.8G>A2.2003e-7-32432Cerebellum
Chr5:96111371ERAP1ENSG00000164307.8G>A1.8079e-8-32432Frontal_Cortex_BA9
Chr5:96111371ERAP1ENSG00000164307.8G>A9.0222e-10-32432Hypothalamus
Chr5:96111371ERAP1ENSG00000164307.8G>A8.4153e-17-32432Cortex
Chr5:96111371ERAP1ENSG00000164307.8G>A3.7415e-13-32432Caudate_basal_ganglia
Chr5:96111371ERAP1ENSG00000164307.8G>A2.8458e-8-32432Brain_Spinal_cord_cervical
Chr5:96111371ERAP1ENSG00000164307.8G>A2.2688e-9-32432Hippocampus
Chr5:96111371ERAP1ENSG00000164307.8G>A4.9729e-7-32432Substantia_nigra
Chr5:96111371ERAP1ENSG00000164307.8G>A6.0046e-11-32432Putamen_basal_ganglia
Chr5:96111371ERAP1ENSG00000164307.8G>A1.3661e-5-32432Anterior_cingulate_cortex
Chr5:96111371ERAP1ENSG00000164307.8G>A2.5895e-6-32432Nucleus_accumbens_basal_ganglia
Chr5:96111371ERAP1ENSG00000164307.8G>A3.3654e-8-32432Amygdala

meQTL of rs13160562 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

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 )
chr59606254196062834E067-48537
chr59610730896107358E067-4013
chr59611214996112193E067778
chr59611232096112697E067949
chr59611277796112843E0671406
chr59612589996126011E06714528
chr59612658096127212E06715209
chr59614185796142327E06730486
chr59606254196062834E068-48537
chr59608796996088235E068-23136
chr59608829196088436E068-22935
chr59610730896107358E068-4013
chr59610891296108991E068-2380
chr59611148896111601E068117
chr59611214996112193E068778
chr59612658096127212E06815209
chr59613852696138649E06827155
chr59613909896139179E06827727
chr59613979696139928E06828425
chr59614147796141557E06830106
chr59614163596141741E06830264
chr59614185796142327E06830486
chr59615327296153684E06841901
chr59611232096112697E069949
chr59611277796112843E0691406
chr59611285796112907E0691486
chr59612589996126011E06914528
chr59612658096127212E06915209
chr59614147796141557E06930106
chr59614163596141741E06930264
chr59614185796142327E06930486
chr59614625896146394E07034887
chr59614672396146777E07035352
chr59614692796146967E07035556
chr59608702196087370E071-24001
chr59608739696087474E071-23897
chr59611148896111601E071117
chr59611214996112193E071778
chr59611232096112697E071949
chr59611277796112843E0711406
chr59611285796112907E0711486
chr59612658096127212E07115209
chr59613944396139532E07128072
chr59614163596141741E07130264
chr59614185796142327E07130486
chr59615327296153684E07141901
chr59615384896154095E07142477
chr59610891296108991E072-2380
chr59610913496109207E072-2164
chr59612658096127212E07215209
chr59613909896139179E07227727
chr59613944396139532E07228072
chr59614163596141741E07230264
chr59614185796142327E07230486
chr59612658096127212E07315209
chr59606254196062834E074-48537
chr59611232096112697E074949
chr59611277796112843E0741406
chr59611285796112907E0741486
chr59611421796114509E0742846
chr59611456996114613E0743198
chr59612589996126011E07414528
chr59612658096127212E07415209
chr59613852696138649E07427155
chr59613909896139179E07427727
chr59613944396139532E07428072
chr59614147796141557E07430106
chr59614163596141741E07430264
chr59614185796142327E07430486
chr59614478296144878E07433411








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr59614269696144582E06731325
chr59614269696144582E06831325
chr59614269696144582E06931325
chr59614269696144582E07031325
chr59614269696144582E07131325
chr59614269696144582E07231325
chr59614269696144582E07331325
chr59614269696144582E07431325
chr59614269696144582E08231325