rs16930262

Homo sapiens
C>T
P4HA1 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0095 (2863/29882,GnomAD)
T=0177 (886/5008,1000G)
T=0057 (221/3854,ALSPAC)
T=0055 (203/3708,TWINSUK)
chr10:73007937 (GRCh38.p7) (10q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.73007937C>T
GRCh37.p13 chr 10NC_000010.10:g.74767695C>T

Gene: P4HA1, prolyl 4-hydroxylase subunit alpha 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
P4HA1 transcript variant 2NM_001017962.2:c.N/A3 Prime UTR Variant
P4HA1 transcript variant 3NM_001142595.1:c.N/A3 Prime UTR Variant
P4HA1 transcript variant 4NM_001142596.1:c.N/A3 Prime UTR Variant
P4HA1 transcript variant 1NM_000917.3:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.831T=0.169
1000GenomesAmericanSub694C=0.900T=0.100
1000GenomesEast AsianSub1008C=0.701T=0.299
1000GenomesEuropeSub1006C=0.946T=0.054
1000GenomesGlobalStudy-wide5008C=0.823T=0.177
1000GenomesSouth AsianSub978C=0.760T=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.943T=0.057
The Genome Aggregation DatabaseAfricanSub8656C=0.852T=0.148
The Genome Aggregation DatabaseAmericanSub836C=0.920T=0.080
The Genome Aggregation DatabaseEast AsianSub1602C=0.748T=0.252
The Genome Aggregation DatabaseEuropeSub18486C=0.941T=0.058
The Genome Aggregation DatabaseGlobalStudy-wide29882C=0.904T=0.095
The Genome Aggregation DatabaseOtherSub302C=0.910T=0.090
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.945T=0.055
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
rs169302620.00049alcohol dependence20201924

eQTL of rs16930262 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:74767695NUDT13ENSG00000166321.9C>T3.0485e-6-102522Cerebellum
Chr10:74767695TTC18ENSG00000156042.13C>T3.0703e-7-350922Cerebellum
Chr10:74767695NUDT13ENSG00000166321.9C>T3.6929e-9-102522Hypothalamus
Chr10:74767695NUDT13ENSG00000166321.9C>T1.5866e-4-102522Cortex
Chr10:74767695NUDT13ENSG00000166321.9C>T1.8918e-5-102522Cerebellar_Hemisphere
Chr10:74767695NUDT13ENSG00000166321.9C>T4.0737e-6-102522Caudate_basal_ganglia
Chr10:74767695NUDT13ENSG00000166321.9C>T1.8681e-6-102522Hippocampus
Chr10:74767695NUDT13ENSG00000166321.9C>T5.7012e-6-102522Putamen_basal_ganglia
Chr10:74767695NUDT13ENSG00000166321.9C>T8.1676e-6-102522Nucleus_accumbens_basal_ganglia

meQTL of rs16930262 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 )
chr107477774574778283E06710050
chr107477838874778726E06710693
chr107477885874778992E06711163
chr107477838874778726E06910693
chr107477885874778992E06911163
chr107477901974779069E06911324
chr107477838874778726E07110693
chr107477885874778992E07111163