rs1729578

Homo sapiens
T>C / T>G
PRKG1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0284 (8495/29908,GnomAD)
C=0246 (7178/29118,TOPMED)
C=0248 (1240/5008,1000G)
C=0299 (1154/3854,ALSPAC)
C=0291 (1078/3708,TWINSUK)
chr10:52223498 (GRCh38.p7) (10q21.1)
AD
GWASCatalog
1   publication(s)
See rs on genome
23 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.52223498T>C
GRCh38.p7 chr 10NC_000010.11:g.52223498T>G
GRCh37.p13 chr 10NC_000010.10:g.53983258T>C
GRCh37.p13 chr 10NC_000010.10:g.53983258T>G
PRKG1 RefSeqGene LRG_1135
PRKG1 RefSeqGene LRG_1135

Gene: PRKG1, protein kinase, cGMP-dependent, type I(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PRKG1 transcript variant 1NM_001098512.2:c.N/AIntron Variant
PRKG1 transcript variant 2NM_006258.3:c.N/AIntron Variant
PRKG1 transcript variant X1XM_017016412.1:c.N/AIntron Variant
PRKG1 transcript variant X2XM_017016413.1:c.N/AIntron Variant
PRKG1 transcript variant X3XM_011539952.2:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.772C=0.228
1000GenomesAmericanSub694T=0.730C=0.270
1000GenomesEast AsianSub1008T=0.836C=0.164
1000GenomesEuropeSub1006T=0.697C=0.303
1000GenomesGlobalStudy-wide5008T=0.752C=0.248
1000GenomesSouth AsianSub978T=0.710C=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.701C=0.299
The Genome Aggregation DatabaseAfricanSub8702T=0.761C=0.239
The Genome Aggregation DatabaseAmericanSub836T=0.710C=0.29,
The Genome Aggregation DatabaseEast AsianSub1612T=0.849C=0.151
The Genome Aggregation DatabaseEuropeSub18456T=0.683C=0.316
The Genome Aggregation DatabaseGlobalStudy-wide29908T=0.715C=0.284
The Genome Aggregation DatabaseOtherSub302T=0.680C=0.32,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.753C=0.246
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.709C=0.291
PMID Title Author Journal
28265120A genome-wide gene-by-trauma interaction study of alcohol misuse in two independent cohorts identifies PRKG1 as a risk locus.Polimanti RMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs17295782E-08alcohol dependence28265120

eQTL of rs1729578 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 rs1729578 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 )
chr102428947824289627E07035782
chr102428984624289896E07036150
chr102428999224290046E07036296
chr102428400424284044E07130308
chr102428407924284149E07130383
chr102428416724284207E07130471
chr102428426824284329E07130572
chr102421933324219744E081-33952
chr102421978824219966E081-33730
chr102429724624298095E08143550
chr102429811024298416E08144414
chr102429842624298649E08144730
chr102429939424299873E08145698
chr102429992624300017E08146230
chr102430006524300115E08146369
chr102421933324219744E082-33952
chr102421978824219966E082-33730
chr102429724624298095E08243550
chr102429811024298416E08244414
chr102429842624298649E08244730
chr102429939424299873E08245698
chr102429992624300017E08246230
chr102430006524300115E08246369




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr102424473324245039E071-8657