rs11688841

Homo sapiens
G>A
AGAP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0022 (671/29976,GnomAD)
A=0034 (1003/29118,TOPMED)
A=0046 (228/5008,1000G)
A=0007 (26/3854,ALSPAC)
A=0007 (25/3708,TWINSUK)
chr2:235887157 (GRCh38.p7) (2q37.2)
AD
GWASdb2
1   publication(s)
See rs on genome
191 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.235887157G>A
GRCh37.p13 chr 2NC_000002.11:g.236795801G>A
AGAP1 RefSeqGeneNG_030314.1:g.398069G>A

Gene: AGAP1, ArfGAP with GTPase domain, ankyrin repeat and PH domain 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
AGAP1 transcript variant 1NM_001037131.2:c.N/AIntron Variant
AGAP1 transcript variant 2NM_014914.4:c.N/AIntron Variant
AGAP1 transcript variant 3NM_001244888.1:c.N/AGenic Downstream Transcript Variant
AGAP1 transcript variant X11XM_005246059.4:c.N/AIntron Variant
AGAP1 transcript variant X8XM_006712234.3:c.N/AIntron Variant
AGAP1 transcript variant X9XM_006712235.3:c.N/AIntron Variant
AGAP1 transcript variant X2XM_006712237.3:c.N/AIntron Variant
AGAP1 transcript variant X1XM_006712239.3:c.N/AIntron Variant
AGAP1 transcript variant X3XM_011510547.2:c.N/AIntron Variant
AGAP1 transcript variant X5XM_011510548.2:c.N/AIntron Variant
AGAP1 transcript variant X7XM_011510549.2:c.N/AIntron Variant
AGAP1 transcript variant X4XM_017003282.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.934A=0.066
1000GenomesAmericanSub694G=0.990A=0.010
1000GenomesEast AsianSub1008G=0.984A=0.016
1000GenomesEuropeSub1006G=0.984A=0.016
1000GenomesGlobalStudy-wide5008G=0.954A=0.046
1000GenomesSouth AsianSub978G=0.900A=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.993A=0.007
The Genome Aggregation DatabaseAfricanSub8710G=0.939A=0.061
The Genome Aggregation DatabaseAmericanSub838G=0.990A=0.010
The Genome Aggregation DatabaseEast AsianSub1620G=0.996A=0.004
The Genome Aggregation DatabaseEuropeSub18506G=0.993A=0.006
The Genome Aggregation DatabaseGlobalStudy-wide29976G=0.977A=0.022
The Genome Aggregation DatabaseOtherSub302G=0.970A=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.965A=0.034
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.993A=0.007
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs116888410.000989alcohol dependence21314694

eQTL of rs11688841 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 rs11688841 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 )
chr2236752645236752819E067-42982
chr2236761245236761592E067-34209
chr2236769602236769702E067-26099
chr2236769703236769806E067-25995
chr2236771835236771885E067-23916
chr2236773790236773919E067-21882
chr2236774010236774064E067-21737
chr2236776966236777168E067-18633
chr2236777459236777572E067-18229
chr2236826250236826559E06730449
chr2236830453236830801E06734652
chr2236842899236843013E06747098
chr2236760209236760268E068-35533
chr2236762782236762916E068-32885
chr2236763056236763248E068-32553
chr2236767677236767727E068-28074
chr2236768180236768224E068-27577
chr2236768249236768620E068-27181
chr2236768651236768865E068-26936
chr2236768876236769031E068-26770
chr2236769045236769248E068-26553
chr2236769602236769702E068-26099
chr2236769703236769806E068-25995
chr2236770128236770307E068-25494
chr2236773113236773180E068-22621
chr2236776966236777168E068-18633
chr2236812442236813408E06816641
chr2236825978236826088E06830177
chr2236826250236826559E06830449
chr2236842735236842804E06846934
chr2236842899236843013E06847098
chr2236843040236843494E06847239
chr2236752645236752819E069-42982
chr2236757623236757972E069-37829
chr2236759820236759923E069-35878
chr2236760209236760268E069-35533
chr2236760837236760903E069-34898
chr2236760941236761006E069-34795
chr2236761245236761592E069-34209
chr2236762782236762916E069-32885
chr2236763056236763248E069-32553
chr2236768249236768620E069-27181
chr2236768651236768865E069-26936
chr2236768876236769031E069-26770
chr2236769045236769248E069-26553
chr2236770975236771105E069-24696
chr2236772294236772346E069-23455
chr2236773113236773180E069-22621
chr2236773476236773644E069-22157
chr2236773790236773919E069-21882
chr2236774010236774064E069-21737
chr2236809957236810177E06914156
chr2236812442236813408E06916641
chr2236825978236826088E06930177
chr2236826250236826559E06930449
chr2236831630236831680E06935829
chr2236842735236842804E06946934
chr2236842899236843013E06947098
chr2236843040236843494E06947239
chr2236757623236757972E070-37829
chr2236760209236760268E070-35533
chr2236761245236761592E070-34209
chr2236773476236773644E070-22157
chr2236773790236773919E070-21882
chr2236812442236813408E07016641
chr2236830192236830413E07034391
chr2236842899236843013E07047098
chr2236843040236843494E07047239
chr2236752645236752819E071-42982
chr2236757623236757972E071-37829
chr2236759820236759923E071-35878
chr2236760209236760268E071-35533
chr2236760837236760903E071-34898
chr2236760941236761006E071-34795
chr2236761245236761592E071-34209
chr2236763056236763248E071-32553
chr2236768249236768620E071-27181
chr2236768651236768865E071-26936
chr2236768876236769031E071-26770
chr2236769045236769248E071-26553
chr2236769602236769702E071-26099
chr2236769703236769806E071-25995
chr2236770128236770307E071-25494
chr2236772294236772346E071-23455
chr2236773113236773180E071-22621
chr2236773476236773644E071-22157
chr2236776966236777168E071-18633
chr2236777459236777572E071-18229
chr2236779922236779972E071-15829
chr2236812442236813408E07116641
chr2236825978236826088E07130177
chr2236826250236826559E07130449
chr2236830453236830801E07134652
chr2236830927236831032E07135126
chr2236831630236831680E07135829
chr2236837525236837659E07141724
chr2236842735236842804E07146934
chr2236842899236843013E07147098
chr2236843040236843494E07147239
chr2236843855236844004E07148054
chr2236752645236752819E072-42982
chr2236759820236759923E072-35878
chr2236760209236760268E072-35533
chr2236760837236760903E072-34898
chr2236760941236761006E072-34795
chr2236761245236761592E072-34209
chr2236762782236762916E072-32885
chr2236763056236763248E072-32553
chr2236767677236767727E072-28074
chr2236768249236768620E072-27181
chr2236768651236768865E072-26936
chr2236768876236769031E072-26770
chr2236769045236769248E072-26553
chr2236769602236769702E072-26099
chr2236772294236772346E072-23455
chr2236773113236773180E072-22621
chr2236776966236777168E072-18633
chr2236795885236795935E07284
chr2236809377236809537E07213576
chr2236809957236810177E07214156
chr2236826250236826559E07230449
chr2236830192236830413E07234391
chr2236830453236830801E07234652
chr2236831630236831680E07235829
chr2236842735236842804E07246934
chr2236842899236843013E07247098
chr2236842735236842804E07346934
chr2236842899236843013E07347098
chr2236752645236752819E074-42982
chr2236759820236759923E074-35878
chr2236760209236760268E074-35533
chr2236760837236760903E074-34898
chr2236760941236761006E074-34795
chr2236761245236761592E074-34209
chr2236762782236762916E074-32885
chr2236763056236763248E074-32553
chr2236767677236767727E074-28074
chr2236768249236768620E074-27181
chr2236768651236768865E074-26936
chr2236768876236769031E074-26770
chr2236770128236770307E074-25494
chr2236773113236773180E074-22621
chr2236773476236773644E074-22157
chr2236773790236773919E074-21882
chr2236774010236774064E074-21737
chr2236776966236777168E074-18633
chr2236777459236777572E074-18229
chr2236808888236809007E07413087
chr2236809377236809537E07413576
chr2236812442236813408E07416641
chr2236815779236815852E07419978
chr2236825978236826088E07430177
chr2236826250236826559E07430449
chr2236831630236831680E07435829
chr2236842735236842804E07446934
chr2236842899236843013E07447098
chr2236843040236843494E07447239
chr2236757623236757972E081-37829
chr2236760209236760268E081-35533
chr2236760837236760903E081-34898
chr2236760941236761006E081-34795
chr2236761245236761592E081-34209
chr2236773476236773644E081-22157
chr2236773790236773919E081-21882
chr2236774010236774064E081-21737
chr2236812442236813408E08116641
chr2236825978236826088E08130177
chr2236826250236826559E08130449
chr2236829228236829412E08133427
chr2236830192236830413E08134391
chr2236830453236830801E08134652
chr2236830927236831032E08135126
chr2236842735236842804E08146934
chr2236842899236843013E08147098
chr2236843040236843494E08147239
chr2236843855236844004E08148054
chr2236844540236844590E08148739
chr2236752645236752819E082-42982
chr2236756280236756452E082-39349
chr2236756875236757018E082-38783
chr2236757623236757972E082-37829
chr2236760837236760903E082-34898
chr2236760941236761006E082-34795
chr2236773476236773644E082-22157
chr2236812442236813408E08216641
chr2236829228236829412E08233427
chr2236830453236830801E08234652
chr2236842899236843013E08247098
chr2236843040236843494E08247239
chr2236843855236844004E08248054
chr2236844540236844590E08248739