rs6709175

Homo sapiens
T>C
ANAPC1P1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0215 (6453/29950,GnomAD)
C=0259 (7550/29116,TOPMED)
C=0191 (957/5008,1000G)
C=0183 (706/3854,ALSPAC)
C=0179 (664/3708,TWINSUK)
chr2:86881088 (GRCh38.p7) (2p11.2)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.86881088T>C
GRCh37.p13 chr 2NC_000002.11:g.87108211T>C

Gene: ANAPC1P1, anaphase promoting complex subunit 1 pseudogene 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ANAPC1P1 transcriptNR_037931.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.583C=0.417
1000GenomesAmericanSub694T=0.850C=0.150
1000GenomesEast AsianSub1008T=0.964C=0.036
1000GenomesEuropeSub1006T=0.836C=0.164
1000GenomesGlobalStudy-wide5008T=0.809C=0.191
1000GenomesSouth AsianSub978T=0.900C=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.817C=0.183
The Genome Aggregation DatabaseAfricanSub8710T=0.623C=0.377
The Genome Aggregation DatabaseAmericanSub838T=0.820C=0.180
The Genome Aggregation DatabaseEast AsianSub1618T=0.954C=0.046
The Genome Aggregation DatabaseEuropeSub18482T=0.843C=0.156
The Genome Aggregation DatabaseGlobalStudy-wide29950T=0.784C=0.215
The Genome Aggregation DatabaseOtherSub302T=0.830C=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.740C=0.259
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.821C=0.179
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs67091753.62E-05alcohol and nictotine co-dependence20158304

eQTL of rs6709175 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:87108211PLGLB1ENSG00000183281.10T>C5.6181e-16-140764Cerebellum
Chr2:87108211PLGLB2ENSG00000125551.14T>C3.9125e-6-939395Cerebellum
Chr2:87108211PLGLB1ENSG00000183281.10T>C3.6408e-5-140764Cortex
Chr2:87108211PLGLB1ENSG00000183281.10T>C4.6577e-7-140764Caudate_basal_ganglia

meQTL of rs6709175 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.