rs1570989

Homo sapiens
A>G
HIVEP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0226 (6779/29952,GnomAD)
A==0218 (6347/29118,TOPMED)
A==0197 (986/5008,1000G)
A==0231 (891/3854,ALSPAC)
A==0232 (861/3708,TWINSUK)
chr6:12048594 (GRCh38.p7) (6p24.1)
AD | ND
GWASdb2 | GWASCatalog
2   publication(s)
See rs on genome
117 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.12048594A>G
GRCh37.p13 chr 6NC_000006.11:g.12048827A>G

Gene: HIVEP1, human immunodeficiency virus type I enhancer binding protein 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
HIVEP1 transcriptNM_002114.3:c.N/AIntron Variant
HIVEP1 transcript variant X1XM_011514546.2:c.N/AIntron Variant
HIVEP1 transcript variant X5XM_011514547.2:c.N/AIntron Variant
HIVEP1 transcript variant X6XM_011514548.2:c.N/AIntron Variant
HIVEP1 transcript variant X7XM_011514549.2:c.N/AIntron Variant
HIVEP1 transcript variant X8XM_011514550.2:c.N/AIntron Variant
HIVEP1 transcript variant X9XM_011514551.2:c.N/AIntron Variant
HIVEP1 transcript variant X10XM_011514552.2:c.N/AIntron Variant
HIVEP1 transcript variant X11XM_011514553.1:c.N/AIntron Variant
HIVEP1 transcript variant X2XM_017010800.1:c.N/AIntron Variant
HIVEP1 transcript variant X3XM_017010801.1:c.N/AIntron Variant
HIVEP1 transcript variant X4XM_017010802.1:c.N/AIntron Variant
HIVEP1 transcript variant X13XM_017010803.1:c.N/AIntron Variant
HIVEP1 transcript variant X15XM_017010804.1:c.N/AIntron Variant
HIVEP1 transcript variant X12XM_011514555.2:c.N/AGenic Upstream Transcript Variant
HIVEP1 transcript variant X14XR_001743372.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.185G=0.815
1000GenomesAmericanSub694A=0.190G=0.810
1000GenomesEast AsianSub1008A=0.187G=0.813
1000GenomesEuropeSub1006A=0.217G=0.783
1000GenomesGlobalStudy-wide5008A=0.197G=0.803
1000GenomesSouth AsianSub978A=0.210G=0.790
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.231G=0.769
The Genome Aggregation DatabaseAfricanSub8714A=0.192G=0.808
The Genome Aggregation DatabaseAmericanSub838A=0.190G=0.810
The Genome Aggregation DatabaseEast AsianSub1618A=0.166G=0.834
The Genome Aggregation DatabaseEuropeSub18480A=0.249G=0.750
The Genome Aggregation DatabaseGlobalStudy-wide29952A=0.226G=0.773
The Genome Aggregation DatabaseOtherSub302A=0.230G=0.770
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.218G=0.782
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.232G=0.768
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs15709890.000002alcohol and nictotine co-dependence22488850
rs15709890.000761alcohol dependence20201924

eQTL of rs1570989 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 rs1570989 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 )
chr61203469712034802E067-14025
chr61203482812034973E067-13854
chr61203506212035386E067-13441
chr61203801912038288E067-10539
chr61204488712044961E067-3866
chr61204506212045631E067-3196
chr61204567812045738E067-3089
chr61205852612058708E0679699
chr61205873112058781E0679904
chr61205887912059030E06710052
chr61206600112066217E06717174
chr61206625812066362E06717431
chr61206665712066833E06717830
chr61208359212083818E06734765
chr61208388712083937E06735060
chr61208415012084239E06735323
chr61209102012091260E06742193
chr61201505712015345E068-33482
chr61203469712034802E068-14025
chr61203482812034973E068-13854
chr61203506212035386E068-13441
chr61204488712044961E068-3866
chr61204506212045631E068-3196
chr61206076212060817E06811935
chr61206600112066217E06817174
chr61206625812066362E06817431
chr61208202212082179E06833195
chr61208236012082410E06833533
chr61208249912082539E06833672
chr61208359212083818E06834765
chr61208388712083937E06835060
chr61208415012084239E06835323
chr61208542912085546E06836602
chr61208587612085972E06837049
chr61209065112090701E06841824
chr61201583512015926E069-32901
chr61202714212027192E069-21635
chr61203469712034802E069-14025
chr61203482812034973E069-13854
chr61203506212035386E069-13441
chr61203991712040040E069-8787
chr61204023212040282E069-8545
chr61204488712044961E069-3866
chr61204506212045631E069-3196
chr61204567812045738E069-3089
chr61205887912059030E06910052
chr61206427912064755E06915452
chr61206494112065237E06916114
chr61206550312065718E06916676
chr61206577712065896E06916950
chr61206600112066217E06917174
chr61206625812066362E06917431
chr61206665712066833E06917830
chr61208359212083818E06934765
chr61208388712083937E06935060
chr61208415012084239E06935323
chr61208542912085546E06936602
chr61200439212004446E070-44381
chr61204023212040282E070-8545
chr61204045512040509E070-8318
chr61204488712044961E070-3866
chr61206076212060817E07011935
chr61206427912064755E07015452
chr61209065112090701E07041824
chr61209102012091260E07042193
chr61209233412092384E07043507
chr61202482612025284E071-23543
chr61202530112025548E071-23279
chr61203469712034802E071-14025
chr61203482812034973E071-13854
chr61203506212035386E071-13441
chr61204488712044961E071-3866
chr61204506212045631E071-3196
chr61206494112065237E07116114
chr61208202212082179E07133195
chr61208236012082410E07133533
chr61208249912082539E07133672
chr61208359212083818E07134765
chr61208388712083937E07135060
chr61208542912085546E07136602
chr61203506212035386E072-13441
chr61204488712044961E072-3866
chr61204506212045631E072-3196
chr61204567812045738E072-3089
chr61206665712066833E07217830
chr61208388712083937E07235060
chr61208415012084239E07235323
chr61208542912085546E07236602
chr61203402512034474E073-14353
chr61203469712034802E073-14025
chr61203482812034973E073-13854
chr61203506212035386E073-13441
chr61203973312039807E073-9020
chr61203991712040040E073-8787
chr61204023212040282E073-8545
chr61204488712044961E073-3866
chr61204506212045631E073-3196
chr61206600112066217E07317174
chr61206625812066362E07317431
chr61208542912085546E07336602
chr61208587612085972E07337049
chr61204506212045631E074-3196
chr61204567812045738E074-3089
chr61206076212060817E07411935
chr61206600112066217E07417174
chr61206625812066362E07417431
chr61208359212083818E07434765
chr61208388712083937E07435060
chr61208415012084239E07435323
chr61204023212040282E081-8545
chr61208542912085546E08136602
chr61203402512034474E082-14353
chr61203469712034802E082-14025
chr61203482812034973E082-13854
chr61203506212035386E082-13441
chr61204488712044961E082-3866
chr61209810012098343E08249273










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr61200779412009972E067-38855
chr61200998012010046E067-38781
chr61201004712014006E067-34821
chr61200779412009972E068-38855
chr61200998012010046E068-38781
chr61201004712014006E068-34821
chr61200779412009972E069-38855
chr61200998012010046E069-38781
chr61201004712014006E069-34821
chr61200779412009972E070-38855
chr61201004712014006E070-34821
chr61200779412009972E071-38855
chr61200998012010046E071-38781
chr61201004712014006E071-34821
chr61200779412009972E072-38855
chr61200998012010046E072-38781
chr61201004712014006E072-34821
chr61200779412009972E073-38855
chr61200998012010046E073-38781
chr61201004712014006E073-34821
chr61200779412009972E074-38855
chr61200998012010046E074-38781
chr61201004712014006E074-34821
chr61200779412009972E081-38855
chr61200998012010046E081-38781
chr61201004712014006E081-34821
chr61200779412009972E082-38855
chr61200998012010046E082-38781
chr61201004712014006E082-34821