rs12716179

Homo sapiens
T>C
FLJ33360 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0131 (3947/29964,GnomAD)
C=0177 (5162/29118,TOPMED)
C=0161 (805/5008,1000G)
C=0035 (135/3854,ALSPAC)
C=0040 (147/3708,TWINSUK)
chr5:6317193 (GRCh38.p7) (5p15.31)
AD
GWASdb2
1   publication(s)
See rs on genome
27 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.6317193T>C
GRCh37.p13 chr 5NC_000005.9:g.6317306T>C

Gene: FLJ33360, FLJ33360 protein(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02145 transcriptNR_028351.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.603C=0.397
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=0.977C=0.023
1000GenomesEuropeSub1006T=0.971C=0.029
1000GenomesGlobalStudy-wide5008T=0.839C=0.161
1000GenomesSouth AsianSub978T=0.810C=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.965C=0.035
The Genome Aggregation DatabaseAfricanSub8714T=0.650C=0.350
The Genome Aggregation DatabaseAmericanSub838T=0.960C=0.040
The Genome Aggregation DatabaseEast AsianSub1620T=0.980C=0.020
The Genome Aggregation DatabaseEuropeSub18490T=0.955C=0.044
The Genome Aggregation DatabaseGlobalStudy-wide29964T=0.868C=0.131
The Genome Aggregation DatabaseOtherSub302T=0.930C=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.822C=0.177
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.960C=0.040
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
rs127161790.00036alcohol dependence(early age of onset)20201924
rs127161790.00059alcohol dependence20201924

eQTL of rs12716179 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 rs12716179 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 )
chr563335896333855E06716283
chr563335896333855E06816283
chr563335896333855E06916283
chr562874116287497E070-29809
chr563021606302551E070-14755
chr563027446302860E070-14446
chr563196606319710E0702354
chr563200606320189E0702754
chr563383946338504E07021088
chr563389406339014E07021634
chr563392506339300E07021944
chr563335896333855E07116283
chr563335896333855E07316283
chr563605736360702E07343267
chr563335896333855E07416283
chr562732456273630E081-43676
chr562764026276790E081-40516
chr562815356281601E081-35705
chr563174576317749E081151
chr563178696318069E081563
chr562732456273630E082-43676
chr562764026276790E082-40516
chr563071266307230E082-10076
chr563174576317749E082151
chr563178696318069E082563
chr563194366319565E0822130
chr563196606319710E0822354