rs12392447

Homo sapiens
A>G
None
Check p-value
SNV (Single Nucleotide Variation)
A=0314 (6231/19830,GnomAD)
A=0397 (1499/3775,1000G)
A=0114 (422/3708,TWINSUK)
A=0119 (343/2889,ALSPAC)
chrX:154496001 (GRCh38.p7) (Xq28)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr XNC_000023.11:g.154496001A>G
GRCh37.p13 chr X fix patch HG1497_PATCHNW_003871103.3:g.1929980A>G
RN7SL697P pseudogeneNG_044023.1:g.213T>C
GRCh37.p13 chr XNC_000023.10:g.153724351G>A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1003G=0.100A==0.900
1000GenomesAmericanSub524G=0.860A==0.140
1000GenomesEast AsianSub764G=0.820A==0.180
1000GenomesEuropeSub766G=0.890A==0.110
1000GenomesGlobalStudy-wide3775G=0.603A==0.397
1000GenomesSouth AsianSub718G=0.580A==0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide2889G=0.881A==0.119
The Genome Aggregation DatabaseAfricanSub5557G=0.186A==0.814
The Genome Aggregation DatabaseAmericanSub606G=0.890A==0.110
The Genome Aggregation DatabaseEast AsianSub1000G=0.830A==0.170
The Genome Aggregation DatabaseEuropeSub12491G=0.885A==0.114
The Genome Aggregation DatabaseGlobalStudy-wide19830G=0.685A==0.314
The Genome Aggregation DatabaseOtherSub176G=0.730A==0.270
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.886A==0.114
PMID Title Author Journal
19581569Genome-wide association study of alcohol dependence.Treutlein JArch Gen Psychiatry

P-Value

SNP ID p-value Traits Study
rs123924472.88E-08alcohol dependence19581569

eQTL of rs12392447 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
ChrX:153724351FAM3AENSG00000071889.12G>A3.3715e-8-20215Cerebellum
ChrX:153724351PLXNA3ENSG00000130827.5G>A2.2025e-1537730Frontal_Cortex_BA9
ChrX:153724351PLXNA3ENSG00000130827.5G>A2.1868e-1137730Cortex
ChrX:153724351PLXNA3ENSG00000130827.5G>A1.0267e-637730Brain_Spinal_cord_cervical
ChrX:153724351PLXNA3ENSG00000130827.5G>A8.9151e-537730Hippocampus
ChrX:153724351PLXNA3ENSG00000130827.5G>A2.6239e-1137730Putamen_basal_ganglia
ChrX:153724351PLXNA3ENSG00000130827.5G>A5.5275e-337730Amygdala

meQTL of rs12392447 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 )
chrX18860331886244E070-43736
chrX18862741886355E070-43625
chrX19326801932815E0702700
chrX19328861933029E0702906
chrX19330831933123E0703103
chrX19797171979957E07249737
chrX18860331886244E081-43736
chrX18862741886355E081-43625
chrX19525991952950E08122619
chrX19530811953187E08123101