rs12629581

Homo sapiens
A>C
CGGBP1 : Intron Variant
ZNF654 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0095 (2876/29982,GnomAD)
C=0075 (2183/29118,TOPMED)
C=0057 (286/5008,1000G)
C=0130 (501/3854,ALSPAC)
C=0124 (460/3708,TWINSUK)
chr3:88122078 (GRCh38.p7) (3p11.1)
AD
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
30 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.88122078A>C
GRCh37.p13 chr 3NC_000003.11:g.88171228A>C

Gene: CGGBP1, CGG triplet repeat binding protein 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CGGBP1 transcript variant 3NM_001195308.1:c.N/AIntron Variant
CGGBP1 transcript variant 1NM_001008390.1:c.N/AGenic Upstream Transcript Variant
CGGBP1 transcript variant 2NM_003663.3:c.N/AGenic Upstream Transcript Variant
CGGBP1 transcript variant X1XM_017007355.1:c.N/AGenic Upstream Transcript Variant

Gene: ZNF654, zinc finger protein 654(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ZNF654 transcriptNM_018293.2:c.N/AGenic Upstream Transcript Variant
ZNF654 transcript variant X5XM_011534340.2:c.N/AIntron Variant
ZNF654 transcript variant X1XM_017006789.1:c.N/AIntron Variant
ZNF654 transcript variant X2XM_017006790.1:c.N/AIntron Variant
ZNF654 transcript variant X3XM_017006791.1:c.N/AIntron Variant
ZNF654 transcript variant X4XM_017006792.1:c.N/AIntron Variant
ZNF654 transcript variant X6XM_017006793.1:c.N/AIntron Variant
ZNF654 transcript variant X7XM_017006794.1:c.N/AIntron Variant
ZNF654 transcript variant X8XM_017006795.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.995C=0.005
1000GenomesAmericanSub694A=0.930C=0.070
1000GenomesEast AsianSub1008A=0.960C=0.040
1000GenomesEuropeSub1006A=0.878C=0.122
1000GenomesGlobalStudy-wide5008A=0.943C=0.057
1000GenomesSouth AsianSub978A=0.930C=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.870C=0.130
The Genome Aggregation DatabaseAfricanSub8732A=0.978C=0.022
The Genome Aggregation DatabaseAmericanSub838A=0.950C=0.050
The Genome Aggregation DatabaseEast AsianSub1618A=0.965C=0.035
The Genome Aggregation DatabaseEuropeSub18492A=0.862C=0.137
The Genome Aggregation DatabaseGlobalStudy-wide29982A=0.904C=0.095
The Genome Aggregation DatabaseOtherSub302A=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.925C=0.075
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.876C=0.124
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs126295810.00098alcohol consumption (maxi-drinks)24277619

eQTL of rs12629581 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr3:88171228CGGBP1ENSG00000163320.6A>C1.6662e-9-27664Cerebellum
Chr3:88171228CGGBP1ENSG00000163320.6A>C3.0644e-6-27664Frontal_Cortex_BA9
Chr3:88171228CGGBP1ENSG00000163320.6A>C2.5859e-3-27664Hypothalamus
Chr3:88171228CGGBP1ENSG00000163320.6A>C8.3817e-5-27664Cortex
Chr3:88171228CGGBP1ENSG00000163320.6A>C7.8899e-5-27664Cerebellar_Hemisphere
Chr3:88171228CGGBP1ENSG00000163320.6A>C1.5647e-3-27664Caudate_basal_ganglia
Chr3:88171228CGGBP1ENSG00000163320.6A>C1.2610e-3-27664Substantia_nigra
Chr3:88171228CGGBP1ENSG00000163320.6A>C2.9940e-4-27664Putamen_basal_ganglia
Chr3:88171228CGGBP1ENSG00000163320.6A>C1.3904e-5-27664Nucleus_accumbens_basal_ganglia

meQTL of rs12629581 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 )
chr38813418688134279E067-36949
chr38818100688181085E0679778
chr38819202488192104E06720796
chr38819219088192290E06720962
chr38812433588124543E068-46685
chr38812499788125037E068-46191
chr38820238088202463E07031152
chr38812433588124543E071-46685
chr38812499788125037E071-46191
chr38818100688181085E0719778
chr38819122988191787E07120001
chr38812433588124543E073-46685
chr38812433588124543E074-46685
chr38814250188142723E074-28505
chr38818100688181085E0749778
chr38819122988191787E07420001
chr38819202488192104E07420796
chr38819219088192290E07420962
chr38820238088202463E08131152







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr38819820588199956E06726977
chr38820002488200420E06728796
chr38820048988200611E06729261
chr38819820588199956E06826977
chr38820002488200420E06828796
chr38820048988200611E06829261
chr38819820588199956E06926977
chr38820002488200420E06928796
chr38820048988200611E06929261
chr38819820588199956E07026977
chr38820002488200420E07028796
chr38820048988200611E07029261
chr38819820588199956E07126977
chr38820002488200420E07128796
chr38820048988200611E07129261
chr38819820588199956E07226977
chr38820002488200420E07228796
chr38820048988200611E07229261
chr38819820588199956E07326977
chr38820002488200420E07328796
chr38820048988200611E07329261
chr38819820588199956E07426977
chr38820002488200420E07428796
chr38820048988200611E07429261
chr38819820588199956E08126977
chr38820002488200420E08128796
chr38820048988200611E08129261
chr38819820588199956E08226977
chr38820002488200420E08228796
chr38820048988200611E08229261