rs2566980

Homo sapiens
A>C
GRAMD1C : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0142 (4261/29922,GnomAD)
C=0174 (5094/29118,TOPMED)
C=0158 (790/5008,1000G)
C=0087 (336/3854,ALSPAC)
C=0076 (280/3708,TWINSUK)
chr3:113841173 (GRCh38.p7) (3q13.31)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.113841173A>C
GRCh37.p13 chr 3NC_000003.11:g.113560020A>C

Gene: GRAMD1C, GRAM domain containing 1C(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GRAMD1C transcript variant 1NM_017577.4:c.N/AIntron Variant
GRAMD1C transcript variant 2NM_001172105.1:c.N/AGenic Upstream Transcript Variant
GRAMD1C transcript variant X2XM_005247546.2:c.N/AIntron Variant
GRAMD1C transcript variant X3XM_005247547.1:c.N/AIntron Variant
GRAMD1C transcript variant X1XM_011512930.1:c.N/AIntron Variant
GRAMD1C transcript variant X4XM_017006646.1:c.N/AIntron Variant
GRAMD1C transcript variant X6XM_017006647.1:c.N/AIntron Variant
GRAMD1C transcript variant X5XM_011512931.1:c.N/AGenic Upstream Transcript Variant
GRAMD1C transcript variant X7XM_017006648.1:c.N/AGenic Upstream Transcript Variant
GRAMD1C transcript variant X8XM_017006649.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.685C=0.315
1000GenomesAmericanSub694A=0.880C=0.120
1000GenomesEast AsianSub1008A=0.937C=0.063
1000GenomesEuropeSub1006A=0.914C=0.086
1000GenomesGlobalStudy-wide5008A=0.842C=0.158
1000GenomesSouth AsianSub978A=0.860C=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.913C=0.087
The Genome Aggregation DatabaseAfricanSub8704A=0.709C=0.291
The Genome Aggregation DatabaseAmericanSub838A=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1618A=0.929C=0.071
The Genome Aggregation DatabaseEuropeSub18460A=0.918C=0.081
The Genome Aggregation DatabaseGlobalStudy-wide29922A=0.857C=0.142
The Genome Aggregation DatabaseOtherSub302A=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.825C=0.174
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.924C=0.076
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
rs25669800.000346alcohol dependence24277619

eQTL of rs2566980 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 rs2566980 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.

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3113557385113558174E067-1846
chr3113558265113558374E067-1646
chr3113557385113558174E068-1846
chr3113558265113558374E068-1646
chr3113557385113558174E069-1846
chr3113558265113558374E069-1646
chr3113558642113558722E069-1298
chr3113558780113558891E069-1129
chr3113557385113558174E070-1846
chr3113558265113558374E070-1646
chr3113557385113558174E071-1846
chr3113558265113558374E071-1646
chr3113558642113558722E071-1298
chr3113558780113558891E071-1129
chr3113557385113558174E072-1846
chr3113558265113558374E072-1646
chr3113558642113558722E072-1298
chr3113558780113558891E072-1129
chr3113557385113558174E073-1846
chr3113558265113558374E073-1646
chr3113557385113558174E074-1846
chr3113558265113558374E074-1646
chr3113558265113558374E081-1646
chr3113557385113558174E082-1846
chr3113558265113558374E082-1646