rs357159

Homo sapiens
G>C
IQSEC1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0322 (9584/29738,GnomAD)
C=0275 (8031/29118,TOPMED)
C=0318 (1594/5008,1000G)
C=0434 (1673/3854,ALSPAC)
C=0405 (1503/3708,TWINSUK)
chr3:13267240 (GRCh38.p7) (3p25.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.13267240G>C
GRCh37.p13 chr 3NC_000003.11:g.13308740G>C

Gene: IQSEC1, IQ motif and Sec7 domain 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
IQSEC1 transcript variant 1NM_001134382.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant 2NM_014869.6:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X1XM_011534304.2:c.N/AIntron Variant
IQSEC1 transcript variant X8XM_011534310.2:c.N/AIntron Variant
IQSEC1 transcript variant X2XM_017007581.1:c.N/AIntron Variant
IQSEC1 transcript variant X3XM_017007582.1:c.N/AIntron Variant
IQSEC1 transcript variant X2XM_011534305.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X5XM_011534306.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X4XM_011534307.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X5XM_011534308.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X7XM_011534311.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X8XM_011534312.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X10XM_011534313.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X9XM_011534314.2:c.N/AGenic Upstream Transcript Variant
IQSEC1 transcript variant X13XM_011534315.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.926C=0.074
1000GenomesAmericanSub694G=0.570C=0.430
1000GenomesEast AsianSub1008G=0.634C=0.366
1000GenomesEuropeSub1006G=0.565C=0.435
1000GenomesGlobalStudy-wide5008G=0.682C=0.318
1000GenomesSouth AsianSub978G=0.600C=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.566C=0.434
The Genome Aggregation DatabaseAfricanSub8640G=0.875C=0.125
The Genome Aggregation DatabaseAmericanSub824G=0.570C=0.430
The Genome Aggregation DatabaseEast AsianSub1598G=0.619C=0.381
The Genome Aggregation DatabaseEuropeSub18374G=0.597C=0.402
The Genome Aggregation DatabaseGlobalStudy-wide29738G=0.677C=0.322
The Genome Aggregation DatabaseOtherSub302G=0.540C=0.460
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.724C=0.275
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.595C=0.405
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
rs3571590.000633alcohol dependence21314694

eQTL of rs357159 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 rs357159 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 )
chr31330150713301558E067-7182
chr31330193713302031E067-6709
chr31330262213302746E067-5994
chr31330304713303120E067-5620
chr31331475213314918E0676012
chr31331497713315064E0676237
chr31331524013315298E0676500
chr31331586913316427E0677129
chr31331818613318319E0679446
chr31331840213318598E0679662
chr31331960613319673E06710866
chr31331991413320009E06711174
chr31334259913342683E06733859
chr31334275113343435E06734011
chr31334991813350305E06741178
chr31335831613358399E06749576
chr31326517113265317E068-43423
chr31326539913265648E068-43092
chr31327335713273522E068-35218
chr31327389313273945E068-34795
chr31327548013275566E068-33174
chr31327556713275734E068-33006
chr31327577513276018E068-32722
chr31328507513285129E068-23611
chr31328532113285490E068-23250
chr31329129213291400E068-17340
chr31329151113291623E068-17117
chr31329164613291821E068-16919
chr31330150713301558E068-7182
chr31330193713302031E068-6709
chr31330262213302746E068-5994
chr31331058413310739E0681844
chr31331079713310930E0682057
chr31331475213314918E0686012
chr31331497713315064E0686237
chr31331524013315298E0686500
chr31331586913316427E0687129
chr31331818613318319E0689446
chr31331840213318598E0689662
chr31331960613319673E06810866
chr31332244013322501E06813700
chr31334259913342683E06833859
chr31334275113343435E06834011
chr31334991813350305E06841178
chr31335831613358399E06849576
chr31327756213277686E069-31054
chr31328507513285129E069-23611
chr31328532113285490E069-23250
chr31330150713301558E069-7182
chr31330193713302031E069-6709
chr31331058413310739E0691844
chr31331079713310930E0692057
chr31331475213314918E0696012
chr31331497713315064E0696237
chr31331524013315298E0696500
chr31331586913316427E0697129
chr31331818613318319E0699446
chr31331960613319673E06910866
chr31331991413320009E06911174
chr31332067713320915E06911937
chr31335831613358399E06949576
chr31327756213277686E070-31054
chr31327810013278150E070-30590
chr31327821113278318E070-30422
chr31328483013284880E070-23860
chr31328507513285129E070-23611
chr31328532113285490E070-23250
chr31329129213291400E070-17340
chr31329151113291623E070-17117
chr31330893913309050E070199
chr31331475213314918E0706012
chr31331497713315064E0706237
chr31331524013315298E0706500
chr31331586913316427E0707129
chr31331924913319336E07010509
chr31331960613319673E07010866
chr31331991413320009E07011174
chr31334259913342683E07033859
chr31334275113343435E07034011
chr31326108113261706E071-47034
chr31328507513285129E071-23611
chr31328532113285490E071-23250
chr31330071113301149E071-7591
chr31330150713301558E071-7182
chr31330193713302031E071-6709
chr31330262213302746E071-5994
chr31331475213314918E0716012
chr31331497713315064E0716237
chr31331524013315298E0716500
chr31331586913316427E0717129
chr31331818613318319E0719446
chr31331840213318598E0719662
chr31331924913319336E07110509
chr31331960613319673E07110866
chr31332228013322340E07113540
chr31332244013322501E07113700
chr31334259913342683E07133859
chr31334275113343435E07134011
chr31335831613358399E07149576
chr31326517113265317E072-43423
chr31326539913265648E072-43092
chr31328532113285490E072-23250
chr31329322113293375E072-15365
chr31330071113301149E072-7591
chr31330150713301558E072-7182
chr31330193713302031E072-6709
chr31331058413310739E0721844
chr31331079713310930E0722057
chr31331475213314918E0726012
chr31331497713315064E0726237
chr31331524013315298E0726500
chr31331586913316427E0727129
chr31331818613318319E0729446
chr31331840213318598E0729662
chr31331960613319673E07210866
chr31331991413320009E07211174
chr31332244013322501E07213700
chr31334275113343435E07234011
chr31335831613358399E07249576
chr31326517113265317E073-43423
chr31329560713295720E073-13020
chr31329607713296157E073-12583
chr31330193713302031E073-6709
chr31330262213302746E073-5994
chr31331497713315064E0736237
chr31331524013315298E0736500
chr31331586913316427E0737129
chr31331818613318319E0739446
chr31331840213318598E0739662
chr31331991413320009E07311174
chr31332244013322501E07313700
chr31334991813350305E07341178
chr31335831613358399E07349576
chr31328483013284880E074-23860
chr31328507513285129E074-23611
chr31328532113285490E074-23250
chr31330150713301558E074-7182
chr31330193713302031E074-6709
chr31331475213314918E0746012
chr31331497713315064E0746237
chr31331524013315298E0746500
chr31331586913316427E0747129
chr31331818613318319E0749446
chr31331840213318598E0749662
chr31331924913319336E07410509
chr31331960613319673E07410866
chr31335831613358399E07449576
chr31327722813277307E081-31433
chr31327821113278318E081-30422
chr31328339413283446E081-25294
chr31329026713290443E081-18297
chr31329129213291400E081-17340
chr31329151113291623E081-17117
chr31329164613291821E081-16919
chr31331058413310739E0811844
chr31331079713310930E0812057
chr31331818613318319E0819446
chr31331840213318598E0819662
chr31331864613319204E0819906
chr31331924913319336E08110509
chr31331960613319673E08110866
chr31333825013338468E08129510
chr31334259913342683E08133859
chr31334275113343435E08134011
chr31329129213291400E082-17340
chr31329151113291623E082-17117
chr31329322113293375E082-15365
chr31329752613297608E082-11132
chr31331058413310739E0821844
chr31331079713310930E0822057
chr31331818613318319E0829446
chr31331840213318598E0829662
chr31331864613319204E0829906
chr31333825013338468E08229510
chr31333914213339229E08230402
chr31334259913342683E08233859
chr31334275113343435E08234011










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr31332309713323344E06714357
chr31332335713323952E06714617
chr31332414113324208E06715401
chr31332430013324440E06715560
chr31332444913324540E06715709
chr31332470213325026E06715962
chr31332518113325371E06716441
chr31332309713323344E06814357
chr31332335713323952E06814617
chr31332414113324208E06815401
chr31332430013324440E06815560
chr31332444913324540E06815709
chr31332470213325026E06815962
chr31332518113325371E06816441
chr31332309713323344E06914357
chr31332335713323952E06914617
chr31332414113324208E06915401
chr31332430013324440E06915560
chr31332444913324540E06915709
chr31332470213325026E06915962
chr31332518113325371E06916441
chr31332414113324208E07015401
chr31332430013324440E07015560
chr31332444913324540E07015709
chr31332470213325026E07015962
chr31332309713323344E07114357
chr31332335713323952E07114617
chr31332414113324208E07115401
chr31332430013324440E07115560
chr31332444913324540E07115709
chr31332470213325026E07115962
chr31332518113325371E07116441
chr31332309713323344E07214357
chr31332335713323952E07214617
chr31332414113324208E07215401
chr31332430013324440E07215560
chr31332444913324540E07215709
chr31332470213325026E07215962
chr31332518113325371E07216441
chr31332309713323344E07314357
chr31332335713323952E07314617
chr31332414113324208E07315401
chr31332430013324440E07315560
chr31332444913324540E07315709
chr31332470213325026E07315962
chr31332518113325371E07316441
chr31332470213325026E07415962
chr31332518113325371E07416441
chr31332309713323344E08214357
chr31332335713323952E08214617
chr31332414113324208E08215401
chr31332430013324440E08215560
chr31332444913324540E08215709
chr31332470213325026E08215962