rs896170

Homo sapiens
T>C
PLXNA4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0216 (6484/29956,GnomAD)
C=0188 (5498/29118,TOPMED)
C=0163 (817/5008,1000G)
C=0278 (1070/3854,ALSPAC)
C=0281 (1041/3708,TWINSUK)
chr7:132180333 (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.132180333T>C
GRCh37.p13 chr 7NC_000007.13:g.131865092T>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
1000GenomesAfricanSub1322T=0.955C=0.045
1000GenomesAmericanSub694T=0.820C=0.180
1000GenomesEast AsianSub1008T=0.878C=0.122
1000GenomesEuropeSub1006T=0.714C=0.286
1000GenomesGlobalStudy-wide5008T=0.837C=0.163
1000GenomesSouth AsianSub978T=0.770C=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.722C=0.278
The Genome Aggregation DatabaseAfricanSub8728T=0.922C=0.078
The Genome Aggregation DatabaseAmericanSub838T=0.810C=0.190
The Genome Aggregation DatabaseEast AsianSub1622T=0.876C=0.124
The Genome Aggregation DatabaseEuropeSub18466T=0.709C=0.290
The Genome Aggregation DatabaseGlobalStudy-wide29956T=0.783C=0.216
The Genome Aggregation DatabaseOtherSub302T=0.710C=0.290
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.811C=0.188
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.719C=0.281
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
rs8961700.000309alcohol dependence20201924

eQTL of rs896170 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 rs896170 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 )
chr7131824892131825282E067-39810
chr7131825393131825569E067-39523
chr7131829948131830001E067-35091
chr7131830013131830097E067-34995
chr7131830162131830629E067-34463
chr7131836810131837186E067-27906
chr7131845356131846405E067-18687
chr7131861840131862016E068-3076
chr7131862056131862145E068-2947
chr7131875288131875338E06810196
chr7131875472131875566E06810380
chr7131829948131830001E069-35091
chr7131830013131830097E069-34995
chr7131830162131830629E069-34463
chr7131845356131846405E069-18687
chr7131845356131846405E070-18687
chr7131846926131847325E070-17767
chr7131847370131847868E070-17224
chr7131861697131861776E070-3316
chr7131861840131862016E070-3076
chr7131862056131862145E070-2947
chr7131862195131862862E070-2230
chr7131862938131863000E070-2092
chr7131863053131863194E070-1898
chr7131863195131863433E070-1659
chr7131899000131899050E07033908
chr7131899054131899270E07033962
chr7131845356131846405E071-18687
chr7131829858131829944E072-35148
chr7131829948131830001E072-35091
chr7131830162131830629E072-34463
chr7131837670131837720E072-27372
chr7131845356131846405E072-18687
chr7131846926131847325E072-17767
chr7131825393131825569E073-39523
chr7131845356131846405E074-18687
chr7131825393131825569E081-39523
chr7131825941131826221E081-38871
chr7131826797131826848E081-38244
chr7131826927131827042E081-38050
chr7131827477131827531E081-37561
chr7131827611131827745E081-37347
chr7131828076131828184E081-36908
chr7131828621131828674E081-36418
chr7131828790131828856E081-36236
chr7131828922131828972E081-36120
chr7131829260131829340E081-35752
chr7131829351131829401E081-35691
chr7131829662131829790E081-35302
chr7131829858131829944E081-35148
chr7131829948131830001E081-35091
chr7131834103131834532E081-30560
chr7131834788131834895E081-30197
chr7131835168131835257E081-29835
chr7131835358131835421E081-29671
chr7131840708131840810E081-24282
chr7131840979131841097E081-23995
chr7131841344131841420E081-23672
chr7131842565131842615E081-22477
chr7131842745131842825E081-22267
chr7131842846131842896E081-22196
chr7131842969131843244E081-21848
chr7131843356131843477E081-21615
chr7131843791131843867E081-21225
chr7131845086131845126E081-19966
chr7131845356131846405E081-18687
chr7131846450131846564E081-18528
chr7131846592131846827E081-18265
chr7131846926131847325E081-17767
chr7131847370131847868E081-17224
chr7131847937131847991E081-17101
chr7131848242131848322E081-16770
chr7131848540131848590E081-16502
chr7131848628131848718E081-16374
chr7131848848131849019E081-16073
chr7131849242131849292E081-15800
chr7131849342131849477E081-15615
chr7131860522131860572E081-4520
chr7131862056131862145E081-2947
chr7131862195131862862E081-2230
chr7131862938131863000E081-2092
chr7131863053131863194E081-1898
chr7131863195131863433E081-1659
chr7131863522131863576E081-1516
chr7131863673131863813E081-1279
chr7131863841131864073E081-1019
chr7131864312131864449E081-643
chr7131867569131867669E0812477
chr7131867684131867734E0812592
chr7131867776131868096E0812684
chr7131868144131868184E0813052
chr7131868245131868843E0813153
chr7131868880131869103E0813788
chr7131911228131911443E08146136
chr7131911578131911638E08146486
chr7131911751131911819E08146659
chr7131911838131911917E08146746
chr7131911999131912065E08146907
chr7131825941131826221E082-38871
chr7131826797131826848E082-38244
chr7131828790131828856E082-36236
chr7131828922131828972E082-36120
chr7131829260131829340E082-35752
chr7131829351131829401E082-35691
chr7131829662131829790E082-35302
chr7131829858131829944E082-35148
chr7131829948131830001E082-35091
chr7131834788131834895E082-30197
chr7131839415131839463E082-25629
chr7131839564131839735E082-25357
chr7131839841131839891E082-25201
chr7131839991131840235E082-24857
chr7131840380131840494E082-24598
chr7131842745131842825E082-22267
chr7131842846131842896E082-22196
chr7131842969131843244E082-21848
chr7131843356131843477E082-21615
chr7131845356131846405E082-18687
chr7131846450131846564E082-18528
chr7131846592131846827E082-18265
chr7131846926131847325E082-17767
chr7131847370131847868E082-17224
chr7131847937131847991E082-17101
chr7131861840131862016E082-3076
chr7131862056131862145E082-2947
chr7131862195131862862E082-2230
chr7131868245131868843E0823153
chr7131868880131869103E0823788
chr7131911999131912065E08246907