rs9871587

Homo sapiens
G>A
TMEM40 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0108 (3247/29950,GnomAD)
A=0142 (4162/29118,TOPMED)
A=0150 (750/5008,1000G)
A=0039 (152/3854,ALSPAC)
A=0040 (147/3708,TWINSUK)
chr3:12755508 (GRCh38.p7) (3p25.2)
AD
GWASdb2
1   publication(s)
See rs on genome
59 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.12755508G>A
GRCh37.p13 chr 3NC_000003.11:g.12797007G>A

Gene: TMEM40, transmembrane protein 40(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TMEM40 transcript variant 1NM_001284406.1:c.N/AIntron Variant
TMEM40 transcript variant 3NM_001284407.1:c.N/AIntron Variant
TMEM40 transcript variant 4NM_001284408.1:c.N/AIntron Variant
TMEM40 transcript variant 2NM_018306.3:c.N/AIntron Variant
TMEM40 transcript variant X1XM_011533937.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.694A=0.306
1000GenomesAmericanSub694G=0.950A=0.050
1000GenomesEast AsianSub1008G=0.826A=0.174
1000GenomesEuropeSub1006G=0.960A=0.040
1000GenomesGlobalStudy-wide5008G=0.850A=0.150
1000GenomesSouth AsianSub978G=0.900A=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.961A=0.039
The Genome Aggregation DatabaseAfricanSub8710G=0.751A=0.249
The Genome Aggregation DatabaseAmericanSub838G=0.950A=0.050
The Genome Aggregation DatabaseEast AsianSub1614G=0.791A=0.209
The Genome Aggregation DatabaseEuropeSub18486G=0.962A=0.037
The Genome Aggregation DatabaseGlobalStudy-wide29950G=0.891A=0.108
The Genome Aggregation DatabaseOtherSub302G=0.970A=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.857A=0.142
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.960A=0.040
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs98715870.000994alcohol dependence20201924

eQTL of rs9871587 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 rs9871587 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 )
chr31279170912792548E067-4459
chr31283735512837415E06740348
chr31283748812837544E06740481
chr31283929112839402E06742284
chr31283947112839592E06742464
chr31283961312839802E06742606
chr31283991612839983E06742909
chr31279170912792548E068-4459
chr31279957312800125E0682566
chr31280014612800220E0683139
chr31280023712800303E0683230
chr31283929112839402E06842284
chr31283947112839592E06842464
chr31283961312839802E06842606
chr31283991612839983E06842909
chr31276123912761291E069-35716
chr31283735512837415E06940348
chr31283748812837544E06940481
chr31283929112839402E06942284
chr31283947112839592E06942464
chr31283961312839802E06942606
chr31283991612839983E06942909
chr31276102212761161E070-35846
chr31279957312800125E0702566
chr31276102212761161E071-35846
chr31283929112839402E07142284
chr31283947112839592E07142464
chr31283929112839402E07342284
chr31283947112839592E07342464
chr31283961312839802E07342606
chr31283991612839983E07342909
chr31275530712755573E081-41434
chr31277022712771134E081-25873
chr31277185912772473E081-24534
chr31277248812772883E081-24124
chr31279957312800125E0812566
chr31280014612800220E0813139
chr31280023712800303E0813230
chr31280177412801955E0814767
chr31280200212802042E0814995
chr31280209412802168E0815087
chr31282668612826875E08129679
chr31283735512837415E08140348
chr31283748812837544E08140481
chr31283929112839402E08142284
chr31283947112839592E08142464
chr31283961312839802E08142606
chr31283991612839983E08142909
chr31276102212761161E082-35846
chr31276211812762204E082-34803
chr31279957312800125E0822566
chr31280014612800220E0823139
chr31280023712800303E0823230
chr31283735512837415E08240348
chr31283748812837544E08240481
chr31283929112839402E08242284
chr31283947112839592E08242464
chr31283961312839802E08242606
chr31283991612839983E08242909








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr31283782512838620E06740818
chr31283868612838982E06741679
chr31283782512838620E06840818
chr31283868612838982E06841679
chr31283782512838620E06940818
chr31283868612838982E06941679
chr31283782512838620E07040818
chr31283868612838982E07041679
chr31283782512838620E07140818
chr31283868612838982E07141679
chr31283782512838620E07240818
chr31283868612838982E07241679
chr31283782512838620E07340818
chr31283868612838982E07341679
chr31283782512838620E07440818
chr31283782512838620E08240818
chr31283868612838982E08241679