rs12425606

Homo sapiens
C>T
PLBD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0248 (7432/29872,GnomAD)
T=0205 (5996/29118,TOPMED)
T=0185 (928/5008,1000G)
T=0280 (1078/3854,ALSPAC)
T=0294 (1090/3708,TWINSUK)
chr12:14562859 (GRCh38.p7) (12p13.1)
ND
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.14562859C>T
GRCh37.p13 chr 12NC_000012.11:g.14715793C>T

Gene: PLBD1, phospholipase B domain containing 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PLBD1 transcriptNM_024829.5:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.935T=0.065
1000GenomesAmericanSub694C=0.660T=0.340
1000GenomesEast AsianSub1008C=0.789T=0.211
1000GenomesEuropeSub1006C=0.685T=0.315
1000GenomesGlobalStudy-wide5008C=0.815T=0.185
1000GenomesSouth AsianSub978C=0.920T=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.720T=0.280
The Genome Aggregation DatabaseAfricanSub8716C=0.910T=0.090
The Genome Aggregation DatabaseAmericanSub836C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1610C=0.799T=0.201
The Genome Aggregation DatabaseEuropeSub18412C=0.675T=0.324
The Genome Aggregation DatabaseGlobalStudy-wide29872C=0.751T=0.248
The Genome Aggregation DatabaseOtherSub298C=0.740T=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.794T=0.205
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.706T=0.294
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs124256060.000115nicotine dependence17158188

eQTL of rs12425606 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 rs12425606 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 )
chr121470685114706905E068-8888
chr121470665214706772E069-9021
chr121470685114706905E069-8888
chr121470694514708005E069-7788
chr121470888214708984E069-6809
chr121470685114706905E071-8888
chr121470694514708005E071-7788
chr121476529114765482E07149498
chr121470685114706905E072-8888
chr121470665214706772E074-9021
chr121470685114706905E074-8888
chr121470694514708005E074-7788
chr121470665214706772E081-9021
chr121470685114706905E081-8888
chr121470694514708005E081-7788






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr121471997614721556E0674183
chr121471997614721556E0684183
chr121471997614721556E0694183
chr121471997614721556E0704183
chr121471997614721556E0714183
chr121471997614721556E0724183
chr121471997614721556E0734183
chr121471997614721556E0744183
chr121471997614721556E0824183