rs4580548

Homo sapiens
C>G / C>T
PTPRG : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0116 (3473/29940,GnomAD)
C==0106 (3104/29118,TOPMED)
C==0113 (568/5008,1000G)
C==0089 (343/3854,ALSPAC)
C==0090 (335/3708,TWINSUK)
chr3:61595375 (GRCh38.p7) (3p14.2)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.61595375C>G
GRCh38.p7 chr 3NC_000003.12:g.61595375C>T
GRCh37.p13 chr 3NC_000003.11:g.61581049C>G
GRCh37.p13 chr 3NC_000003.11:g.61581049C>T

Gene: PTPRG, protein tyrosine phosphatase, receptor type G(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PTPRG transcriptNM_002841.3:c.N/AIntron Variant
PTPRG transcript variant X4XM_005265353.3:c.N/AIntron Variant
PTPRG transcript variant X1XM_017006961.1:c.N/AIntron Variant
PTPRG transcript variant X3XM_017006963.1:c.N/AIntron Variant
PTPRG transcript variant X2XM_017006962.1:c.N/AGenic Upstream Transcript Variant
PTPRG transcript variant X5XM_017006964.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.115G=0.885
1000GenomesAmericanSub694C=0.080G=0.920
1000GenomesEast AsianSub1008C=0.228G=0.772
1000GenomesEuropeSub1006C=0.102G=0.898
1000GenomesGlobalStudy-wide5008C=0.113G=0.887
1000GenomesSouth AsianSub978C=0.030G=0.970
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.089G=0.911
The Genome Aggregation DatabaseAfricanSub8722C=0.120G=0.880
The Genome Aggregation DatabaseAmericanSub838C=0.100G=0.90,
The Genome Aggregation DatabaseEast AsianSub1616C=0.218G=0.782
The Genome Aggregation DatabaseEuropeSub18462C=0.106G=0.893
The Genome Aggregation DatabaseGlobalStudy-wide29940C=0.116G=0.884
The Genome Aggregation DatabaseOtherSub302C=0.090G=0.91,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.106G=0.893
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.090G=0.910
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs45805480.000996alcohol dependence21314694

eQTL of rs4580548 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 rs4580548 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 )
chr37993352379933843E08123205
chr37993410179934175E08123783
chr37992067379920730E08210355
chr37992089479920963E08210576
chr37993352379933843E08223205