rs17427389

Homo sapiens
G>A
PLEKHG1 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0155 (4643/29780,GnomAD)
A=0116 (3402/29118,TOPMED)
A=0143 (714/5008,1000G)
A=0178 (687/3854,ALSPAC)
A=0188 (696/3708,TWINSUK)
chr6:150841979 (GRCh38.p7) (6q25.1)
AD | ND
GWASdb2 | GWASCatalog
3   publication(s)
See rs on genome
49 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.150841979G>A
GRCh37.p13 chr 6NC_000006.11:g.151163115G>A

Gene: PLEKHG1, pleckstrin homology and RhoGEF domain containing G1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PLEKHG1 transcriptNM_001029884.1:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X4XM_006715521.1:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X1XM_011535981.2:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X2XM_005267064.3:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X3XM_011535982.2:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X5XM_005267065.3:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X6XM_011535983.2:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X7XM_005267066.2:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X8XM_006715522.3:c.N/A3 Prime UTR Variant
PLEKHG1 transcript variant X9XM_017011102.1:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.956A=0.044
1000GenomesAmericanSub694G=0.770A=0.230
1000GenomesEast AsianSub1008G=0.874A=0.126
1000GenomesEuropeSub1006G=0.846A=0.154
1000GenomesGlobalStudy-wide5008G=0.857A=0.143
1000GenomesSouth AsianSub978G=0.780A=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.822A=0.178
The Genome Aggregation DatabaseAfricanSub8686G=0.953A=0.047
The Genome Aggregation DatabaseAmericanSub836G=0.780A=0.220
The Genome Aggregation DatabaseEast AsianSub1616G=0.863A=0.137
The Genome Aggregation DatabaseEuropeSub18340G=0.793A=0.206
The Genome Aggregation DatabaseGlobalStudy-wide29780G=0.844A=0.155
The Genome Aggregation DatabaseOtherSub302G=0.840A=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.883A=0.116
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.812A=0.188
PMID Title Author Journal
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs174273890.000001alcohol and nicotine co-dependence22488850
rs174273890.00000645alcohol dependence20202923
rs174273890.0000072alcohol dependence21956439

eQTL of rs17427389 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 rs17427389 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 )
chr6151134412151135671E067-27444
chr6151197049151198272E06733934
chr6151202642151202815E06739527
chr6151202853151203863E06739738
chr6151167494151167547E0684379
chr6151197049151198272E06833934
chr6151202642151202815E06839527
chr6151202853151203863E06839738
chr6151167494151167547E0694379
chr6151167893151168120E0694778
chr6151197049151198272E06933934
chr6151202642151202815E06939527
chr6151202853151203863E06939738
chr6151197049151198272E07033934
chr6151201363151201614E07038248
chr6151201628151201742E07038513
chr6151202853151203863E07039738
chr6151203900151204190E07040785
chr6151202853151203863E07139738
chr6151197049151198272E07233934
chr6151202853151203863E07239738
chr6151202853151203863E07339738
chr6151121778151122528E074-40587
chr6151167494151167547E0744379
chr6151167893151168120E0744778
chr6151177820151179584E07414705
chr6151197049151198272E07433934
chr6151202853151203863E07439738
chr6151121778151122528E081-40587
chr6151133806151133926E081-29189
chr6151195054151195102E08131939
chr6151195168151195649E08132053
chr6151195757151195835E08132642
chr6151196057151196097E08132942
chr6151196268151196402E08133153
chr6151196592151196674E08133477
chr6151197049151198272E08133934
chr6151198421151198578E08135306
chr6151198630151198699E08135515
chr6151198712151198779E08135597
chr6151198816151198866E08135701
chr6151198913151198988E08135798
chr6151198996151199119E08135881
chr6151199148151199299E08136033
chr6151202853151203863E08139738
chr6151196268151196402E08233153
chr6151196592151196674E08233477
chr6151197049151198272E08233934
chr6151198421151198578E08235306










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr6151186126151188882E06723011
chr6151186126151188882E06823011
chr6151186126151188882E06923011
chr6151186126151188882E07023011
chr6151186126151188882E07123011
chr6151186126151188882E07223011
chr6151186126151188882E07323011
chr6151186126151188882E07423011
chr6151186126151188882E08123011
chr6151186126151188882E08223011