rs11706542

Homo sapiens
C>T
CMC1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0235 (7036/29900,GnomAD)
T=0209 (6107/29118,TOPMED)
T=0163 (816/5008,1000G)
T=0279 (1075/3854,ALSPAC)
T=0287 (1064/3708,TWINSUK)
chr3:28287092 (GRCh38.p7) (3p24.1)
AD
GWASdb2
2   publication(s)
See rs on genome
5 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.28287092C>T
GRCh37.p13 chr 3NC_000003.11:g.28328583C>T

Gene: CMC1, C-x9-C motif containing 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CMC1 transcript variant 4NM_182523.1:c.N/AIntron Variant
CMC1 transcript variant X1XM_011533402.2:c.N/AIntron Variant
CMC1 transcript variant X8XM_017005760.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.930T=0.070
1000GenomesAmericanSub694C=0.780T=0.220
1000GenomesEast AsianSub1008C=0.839T=0.161
1000GenomesEuropeSub1006C=0.699T=0.301
1000GenomesGlobalStudy-wide5008C=0.837T=0.163
1000GenomesSouth AsianSub978C=0.890T=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.721T=0.279
The Genome Aggregation DatabaseAfricanSub8710C=0.882T=0.118
The Genome Aggregation DatabaseAmericanSub838C=0.790T=0.210
The Genome Aggregation DatabaseEast AsianSub1614C=0.810T=0.190
The Genome Aggregation DatabaseEuropeSub18436C=0.706T=0.293
The Genome Aggregation DatabaseGlobalStudy-wide29900C=0.764T=0.235
The Genome Aggregation DatabaseOtherSub302C=0.640T=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.790T=0.209
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.713T=0.287
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
19581569Genome-wide association study of alcohol dependence.Treutlein JArch Gen Psychiatry

P-Value

SNP ID p-value Traits Study
rs117065429.43E-05alcohol dependence19581569

eQTL of rs11706542 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 rs11706542 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 )
chr32835945228359534E06830869
chr32830733728307392E070-21191
chr32828527928285493E071-43090
chr32829644828296600E074-31983
chr32833696528337910E0818382





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr32828249028283915E067-44668
chr32828249028283915E068-44668
chr32828249028283915E069-44668
chr32828249028283915E070-44668
chr32828249028283915E071-44668
chr32828249028283915E072-44668
chr32828249028283915E073-44668
chr32828249028283915E074-44668
chr32828249028283915E081-44668
chr32828249028283915E082-44668