rs10031299

Homo sapiens
T>C
PCAT4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0218 (6540/29894,GnomAD)
C=0237 (6912/29118,TOPMED)
C=0225 (1126/5008,1000G)
C=0148 (571/3854,ALSPAC)
C=0151 (559/3708,TWINSUK)
chr4:79832638 (GRCh38.p7) (4q21.21)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.79832638T>C
GRCh37.p13 chr 4NC_000004.11:g.80753792T>C

Gene: PCAT4, prostate cancer associated transcript 4 (non-protein coding)(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PCAT4 transcriptNR_026555.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.617C=0.383
1000GenomesAmericanSub694T=0.810C=0.190
1000GenomesEast AsianSub1008T=0.712C=0.288
1000GenomesEuropeSub1006T=0.860C=0.140
1000GenomesGlobalStudy-wide5008T=0.775C=0.225
1000GenomesSouth AsianSub978T=0.940C=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.852C=0.148
The Genome Aggregation DatabaseAfricanSub8688T=0.646C=0.354
The Genome Aggregation DatabaseAmericanSub838T=0.750C=0.250
The Genome Aggregation DatabaseEast AsianSub1612T=0.679C=0.321
The Genome Aggregation DatabaseEuropeSub18454T=0.854C=0.145
The Genome Aggregation DatabaseGlobalStudy-wide29894T=0.781C=0.218
The Genome Aggregation DatabaseOtherSub302T=0.810C=0.190
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.762C=0.237
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.849C=0.151
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs100312990.000669alcohol dependence20201924

eQTL of rs10031299 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 rs10031299 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 )
chr48077517480775230E08121382
chr48077538680775692E08121594