rs3734989

Homo sapiens
T>C
PLXNA4 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0323 (37540/116218,ExAC)
T==0307 (9204/29934,GnomAD)
T==0253 (7373/29118,TOPMED)
C=0282 (3650/12944,GO-ESP)
T==0218 (1090/5008,1000G)
T==0396 (1527/3854,ALSPAC)
T==0406 (1504/3708,TWINSUK)
chr7:132179832 (GRCh38.p7) (7q32.3)
AD
GWASdb2
1   publication(s)
See rs on genome
129 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.132179832T>C
GRCh37.p13 chr 7NC_000007.13:g.131864591T>C

Gene: PLXNA4, plexin A4(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PLXNA4 transcript variant 3NM_001105543.1:c.N/AGenic Downstream Transcript Variant
PLXNA4 transcript variant 2NM_181775.3:c.N/AGenic Downstream Transcript Variant
PLXNA4 transcript variant 1NM_020911.1:c.372...NM_020911.1:c.3729A>GA [GCA]> A [GCG]Coding Sequence Variant
plexin-A4 isoform 1 precursorNP_065962.1:p.Ala...NP_065962.1:p.Ala1243=A [Ala]> A [Ala]Synonymous Variant
PLXNA4 transcript variant X1XM_006716171.3:c....XM_006716171.3:c.3729A>GA [GCA]> A [GCG]Coding Sequence Variant
plexin-A4 isoform X1XP_006716234.1:p....XP_006716234.1:p.Ala1243=A [Ala]> A [Ala]Synonymous Variant
PLXNA4 transcript variant X2XM_005250686.4:c....XM_005250686.4:c.3729A>GA [GCA]> A [GCG]Coding Sequence Variant
plexin-A4 isoform X1XP_005250743.1:p....XP_005250743.1:p.Ala1243=A [Ala]> A [Ala]Synonymous Variant
PLXNA4 transcript variant X3XM_017012779.1:c....XM_017012779.1:c.3528A>GA [GCA]> A [GCG]Coding Sequence Variant
plexin-A4 isoform X2XP_016868268.1:p....XP_016868268.1:p.Ala1176=A [Ala]> A [Ala]Synonymous Variant
PLXNA4 transcript variant X4XM_011516676.2:c....XM_011516676.2:c.3729A>GA [GCA]> A [GCG]Coding Sequence Variant
plexin-A4 isoform X3XP_011514978.1:p....XP_011514978.1:p.Ala1243=A [Ala]> A [Ala]Synonymous Variant
PLXNA4 transcript variant X5XR_927546.2:n.386...XR_927546.2:n.3864A>GA>GNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.020C=0.980
1000GenomesAmericanSub694T=0.270C=0.730
1000GenomesEast AsianSub1008T=0.367C=0.633
1000GenomesEuropeSub1006T=0.387C=0.613
1000GenomesGlobalStudy-wide5008T=0.218C=0.782
1000GenomesSouth AsianSub978T=0.120C=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.396C=0.604
The Exome Aggregation ConsortiumAmericanSub20636T=0.207C=0.792
The Exome Aggregation ConsortiumAsianSub24826T=0.220C=0.779
The Exome Aggregation ConsortiumEuropeSub69898T=0.393C=0.606
The Exome Aggregation ConsortiumGlobalStudy-wide116218T=0.323C=0.676
The Exome Aggregation ConsortiumOtherSub858T=0.350C=0.650
The Genome Aggregation DatabaseAfricanSub8720T=0.075C=0.925
The Genome Aggregation DatabaseAmericanSub834T=0.330C=0.670
The Genome Aggregation DatabaseEast AsianSub1618T=0.354C=0.646
The Genome Aggregation DatabaseEuropeSub18460T=0.412C=0.587
The Genome Aggregation DatabaseGlobalStudy-wide29934T=0.307C=0.692
The Genome Aggregation DatabaseOtherSub302T=0.280C=0.720
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.253C=0.746
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.406C=0.594
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs37349892.01E-05alcohol consumption23743675

eQTL of rs3734989 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 rs3734989 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 )
chr7131824892131825282E067-39309
chr7131825393131825569E067-39022
chr7131829948131830001E067-34590
chr7131830013131830097E067-34494
chr7131830162131830629E067-33962
chr7131836810131837186E067-27405
chr7131845356131846405E067-18186
chr7131861840131862016E068-2575
chr7131862056131862145E068-2446
chr7131875288131875338E06810697
chr7131875472131875566E06810881
chr7131829948131830001E069-34590
chr7131830013131830097E069-34494
chr7131830162131830629E069-33962
chr7131845356131846405E069-18186
chr7131845356131846405E070-18186
chr7131846926131847325E070-17266
chr7131847370131847868E070-16723
chr7131861697131861776E070-2815
chr7131861840131862016E070-2575
chr7131862056131862145E070-2446
chr7131862195131862862E070-1729
chr7131862938131863000E070-1591
chr7131863053131863194E070-1397
chr7131863195131863433E070-1158
chr7131899000131899050E07034409
chr7131899054131899270E07034463
chr7131845356131846405E071-18186
chr7131829858131829944E072-34647
chr7131829948131830001E072-34590
chr7131830162131830629E072-33962
chr7131837670131837720E072-26871
chr7131845356131846405E072-18186
chr7131846926131847325E072-17266
chr7131825393131825569E073-39022
chr7131845356131846405E074-18186
chr7131825393131825569E081-39022
chr7131825941131826221E081-38370
chr7131826797131826848E081-37743
chr7131826927131827042E081-37549
chr7131827477131827531E081-37060
chr7131827611131827745E081-36846
chr7131828076131828184E081-36407
chr7131828621131828674E081-35917
chr7131828790131828856E081-35735
chr7131828922131828972E081-35619
chr7131829260131829340E081-35251
chr7131829351131829401E081-35190
chr7131829662131829790E081-34801
chr7131829858131829944E081-34647
chr7131829948131830001E081-34590
chr7131834103131834532E081-30059
chr7131834788131834895E081-29696
chr7131835168131835257E081-29334
chr7131835358131835421E081-29170
chr7131840708131840810E081-23781
chr7131840979131841097E081-23494
chr7131841344131841420E081-23171
chr7131842565131842615E081-21976
chr7131842745131842825E081-21766
chr7131842846131842896E081-21695
chr7131842969131843244E081-21347
chr7131843356131843477E081-21114
chr7131843791131843867E081-20724
chr7131845086131845126E081-19465
chr7131845356131846405E081-18186
chr7131846450131846564E081-18027
chr7131846592131846827E081-17764
chr7131846926131847325E081-17266
chr7131847370131847868E081-16723
chr7131847937131847991E081-16600
chr7131848242131848322E081-16269
chr7131848540131848590E081-16001
chr7131848628131848718E081-15873
chr7131848848131849019E081-15572
chr7131849242131849292E081-15299
chr7131849342131849477E081-15114
chr7131860522131860572E081-4019
chr7131862056131862145E081-2446
chr7131862195131862862E081-1729
chr7131862938131863000E081-1591
chr7131863053131863194E081-1397
chr7131863195131863433E081-1158
chr7131863522131863576E081-1015
chr7131863673131863813E081-778
chr7131863841131864073E081-518
chr7131864312131864449E081-142
chr7131867569131867669E0812978
chr7131867684131867734E0813093
chr7131867776131868096E0813185
chr7131868144131868184E0813553
chr7131868245131868843E0813654
chr7131868880131869103E0814289
chr7131911228131911443E08146637
chr7131911578131911638E08146987
chr7131911751131911819E08147160
chr7131911838131911917E08147247
chr7131911999131912065E08147408
chr7131825941131826221E082-38370
chr7131826797131826848E082-37743
chr7131828790131828856E082-35735
chr7131828922131828972E082-35619
chr7131829260131829340E082-35251
chr7131829351131829401E082-35190
chr7131829662131829790E082-34801
chr7131829858131829944E082-34647
chr7131829948131830001E082-34590
chr7131834788131834895E082-29696
chr7131839415131839463E082-25128
chr7131839564131839735E082-24856
chr7131839841131839891E082-24700
chr7131839991131840235E082-24356
chr7131840380131840494E082-24097
chr7131842745131842825E082-21766
chr7131842846131842896E082-21695
chr7131842969131843244E082-21347
chr7131843356131843477E082-21114
chr7131845356131846405E082-18186
chr7131846450131846564E082-18027
chr7131846592131846827E082-17764
chr7131846926131847325E082-17266
chr7131847370131847868E082-16723
chr7131847937131847991E082-16600
chr7131861840131862016E082-2575
chr7131862056131862145E082-2446
chr7131862195131862862E082-1729
chr7131868245131868843E0823654
chr7131868880131869103E0824289
chr7131911999131912065E08247408