rs6946056

Homo sapiens
A>C
PLXNA4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0301 (9016/29878,GnomAD)
A==0252 (7365/29118,TOPMED)
A==0215 (1078/5008,1000G)
A==0394 (1520/3854,ALSPAC)
A==0400 (1485/3708,TWINSUK)
chr7:132185838 (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.132185838A>C
GRCh37.p13 chr 7NC_000007.13:g.131870597A>C

Gene: PLXNA4, plexin A4(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PLXNA4 transcript variant 1NM_020911.1:c.N/AIntron Variant
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 X2XM_005250686.4:c.N/AIntron Variant
PLXNA4 transcript variant X1XM_006716171.3:c.N/AIntron Variant
PLXNA4 transcript variant X4XM_011516676.2:c.N/AIntron Variant
PLXNA4 transcript variant X3XM_017012779.1:c.N/AIntron Variant
PLXNA4 transcript variant X5XR_927546.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.020C=0.980
1000GenomesAmericanSub694A=0.280C=0.720
1000GenomesEast AsianSub1008A=0.342C=0.658
1000GenomesEuropeSub1006A=0.380C=0.620
1000GenomesGlobalStudy-wide5008A=0.215C=0.785
1000GenomesSouth AsianSub978A=0.130C=0.870
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.394C=0.606
The Genome Aggregation DatabaseAfricanSub8708A=0.072C=0.928
The Genome Aggregation DatabaseAmericanSub838A=0.330C=0.670
The Genome Aggregation DatabaseEast AsianSub1612A=0.331C=0.669
The Genome Aggregation DatabaseEuropeSub18418A=0.407C=0.592
The Genome Aggregation DatabaseGlobalStudy-wide29878A=0.301C=0.698
The Genome Aggregation DatabaseOtherSub302A=0.270C=0.730
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.252C=0.747
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.400C=0.600
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
rs69460560.000147alcohol consumption23743675

eQTL of rs6946056 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 rs6946056 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 )
chr7131824892131825282E067-45315
chr7131825393131825569E067-45028
chr7131829948131830001E067-40596
chr7131830013131830097E067-40500
chr7131830162131830629E067-39968
chr7131836810131837186E067-33411
chr7131845356131846405E067-24192
chr7131861840131862016E068-8581
chr7131862056131862145E068-8452
chr7131875288131875338E0684691
chr7131875472131875566E0684875
chr7131829948131830001E069-40596
chr7131830013131830097E069-40500
chr7131830162131830629E069-39968
chr7131845356131846405E069-24192
chr7131845356131846405E070-24192
chr7131846926131847325E070-23272
chr7131847370131847868E070-22729
chr7131861697131861776E070-8821
chr7131861840131862016E070-8581
chr7131862056131862145E070-8452
chr7131862195131862862E070-7735
chr7131862938131863000E070-7597
chr7131863053131863194E070-7403
chr7131863195131863433E070-7164
chr7131899000131899050E07028403
chr7131899054131899270E07028457
chr7131845356131846405E071-24192
chr7131829858131829944E072-40653
chr7131829948131830001E072-40596
chr7131830162131830629E072-39968
chr7131837670131837720E072-32877
chr7131845356131846405E072-24192
chr7131846926131847325E072-23272
chr7131825393131825569E073-45028
chr7131845356131846405E074-24192
chr7131825393131825569E081-45028
chr7131825941131826221E081-44376
chr7131826797131826848E081-43749
chr7131826927131827042E081-43555
chr7131827477131827531E081-43066
chr7131827611131827745E081-42852
chr7131828076131828184E081-42413
chr7131828621131828674E081-41923
chr7131828790131828856E081-41741
chr7131828922131828972E081-41625
chr7131829260131829340E081-41257
chr7131829351131829401E081-41196
chr7131829662131829790E081-40807
chr7131829858131829944E081-40653
chr7131829948131830001E081-40596
chr7131834103131834532E081-36065
chr7131834788131834895E081-35702
chr7131835168131835257E081-35340
chr7131835358131835421E081-35176
chr7131840708131840810E081-29787
chr7131840979131841097E081-29500
chr7131841344131841420E081-29177
chr7131842565131842615E081-27982
chr7131842745131842825E081-27772
chr7131842846131842896E081-27701
chr7131842969131843244E081-27353
chr7131843356131843477E081-27120
chr7131843791131843867E081-26730
chr7131845086131845126E081-25471
chr7131845356131846405E081-24192
chr7131846450131846564E081-24033
chr7131846592131846827E081-23770
chr7131846926131847325E081-23272
chr7131847370131847868E081-22729
chr7131847937131847991E081-22606
chr7131848242131848322E081-22275
chr7131848540131848590E081-22007
chr7131848628131848718E081-21879
chr7131848848131849019E081-21578
chr7131849242131849292E081-21305
chr7131849342131849477E081-21120
chr7131860522131860572E081-10025
chr7131862056131862145E081-8452
chr7131862195131862862E081-7735
chr7131862938131863000E081-7597
chr7131863053131863194E081-7403
chr7131863195131863433E081-7164
chr7131863522131863576E081-7021
chr7131863673131863813E081-6784
chr7131863841131864073E081-6524
chr7131864312131864449E081-6148
chr7131867569131867669E081-2928
chr7131867684131867734E081-2863
chr7131867776131868096E081-2501
chr7131868144131868184E081-2413
chr7131868245131868843E081-1754
chr7131868880131869103E081-1494
chr7131911228131911443E08140631
chr7131911578131911638E08140981
chr7131911751131911819E08141154
chr7131911838131911917E08141241
chr7131911999131912065E08141402
chr7131825941131826221E082-44376
chr7131826797131826848E082-43749
chr7131828790131828856E082-41741
chr7131828922131828972E082-41625
chr7131829260131829340E082-41257
chr7131829351131829401E082-41196
chr7131829662131829790E082-40807
chr7131829858131829944E082-40653
chr7131829948131830001E082-40596
chr7131834788131834895E082-35702
chr7131839415131839463E082-31134
chr7131839564131839735E082-30862
chr7131839841131839891E082-30706
chr7131839991131840235E082-30362
chr7131840380131840494E082-30103
chr7131842745131842825E082-27772
chr7131842846131842896E082-27701
chr7131842969131843244E082-27353
chr7131843356131843477E082-27120
chr7131845356131846405E082-24192
chr7131846450131846564E082-24033
chr7131846592131846827E082-23770
chr7131846926131847325E082-23272
chr7131847370131847868E082-22729
chr7131847937131847991E082-22606
chr7131861840131862016E082-8581
chr7131862056131862145E082-8452
chr7131862195131862862E082-7735
chr7131868245131868843E082-1754
chr7131868880131869103E082-1494
chr7131911999131912065E08241402