rs9841007

Homo sapiens
T>C
PCOLCE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0356 (10674/29930,GnomAD)
C=0411 (11995/29118,TOPMED)
C=0343 (1716/5008,1000G)
C=0232 (893/3854,ALSPAC)
C=0246 (913/3708,TWINSUK)
chr3:142822845 (GRCh38.p7) (3q23)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.142822845T>C
GRCh37.p13 chr 3NC_000003.11:g.142541687T>C

Gene: PCOLCE2, procollagen C-endopeptidase enhancer 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PCOLCE2 transcriptNM_013363.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.338C=0.662
1000GenomesAmericanSub694T=0.810C=0.190
1000GenomesEast AsianSub1008T=0.708C=0.292
1000GenomesEuropeSub1006T=0.739C=0.261
1000GenomesGlobalStudy-wide5008T=0.657C=0.343
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.768C=0.232
The Genome Aggregation DatabaseAfricanSub8698T=0.376C=0.624
The Genome Aggregation DatabaseAmericanSub834T=0.770C=0.230
The Genome Aggregation DatabaseEast AsianSub1620T=0.691C=0.309
The Genome Aggregation DatabaseEuropeSub18476T=0.755C=0.244
The Genome Aggregation DatabaseGlobalStudy-wide29930T=0.643C=0.356
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.588C=0.411
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.754C=0.246
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
rs98410070.000152alcohol dependence20201924

eQTL of rs9841007 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr3:142541687RP11-343B5.1ENSG00000233597.3T>C1.6343e-2778647Nucleus_accumbens_basal_ganglia

meQTL of rs9841007 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 )
chr3142527005142527380E067-14307
chr3142527005142527380E068-14307
chr3142527005142527380E069-14307
chr3142527005142527380E072-14307
chr3142527005142527380E074-14307
chr3142580542142580675E08138855
chr3142580719142580844E08139032
chr3142580915142581329E08139228
chr3142581924142583097E08140237