rs12123554

Homo sapiens
T>C
LOC105371458 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0089 (2685/29976,GnomAD)
C=0072 (2113/29118,TOPMED)
C=0040 (202/5008,1000G)
C=0117 (450/3854,ALSPAC)
C=0109 (406/3708,TWINSUK)
chr1:157935353 (GRCh38.p7) (1q23.1)
AD
GWASdb2
1   publication(s)
See rs on genome
10 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.157935353T>C
GRCh37.p13 chr 1NC_000001.10:g.157905143T>C

Gene: LOC105371458, uncharacterized LOC105371458(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105371458 transcriptNR_135760.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.996C=0.004
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.871C=0.129
1000GenomesGlobalStudy-wide5008T=0.960C=0.040
1000GenomesSouth AsianSub978T=0.970C=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.883C=0.117
The Genome Aggregation DatabaseAfricanSub8724T=0.978C=0.022
The Genome Aggregation DatabaseAmericanSub834T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1622T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18494T=0.868C=0.131
The Genome Aggregation DatabaseGlobalStudy-wide29976T=0.910C=0.089
The Genome Aggregation DatabaseOtherSub302T=0.930C=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.927C=0.072
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.891C=0.109
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
rs121235540.0000548alcoholismpha002892
rs121235540.000055alcohol dependence20201924

eQTL of rs12123554 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 rs12123554 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 )
chr1157933523157933875E06828380
chr1157933922157934140E06828779
chr1157935394157936568E07030251
chr1157938152157939465E07033009
chr1157944606157944666E07039463
chr1157944688157944768E07039545
chr1157945040157945313E07039897
chr1157945589157945692E07040446
chr1157947252157947350E07042109
chr1157938152157939465E08133009



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1157948468157948617E06843325
chr1157948468157948617E07043325
chr1157948468157948617E07143325
chr1157948468157948617E08243325