rs2439353

Homo sapiens
C>G / C>T
LINC01169 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0377 (11283/29924,GnomAD)
C==0365 (10654/29118,TOPMED)
C==0432 (2163/5008,1000G)
C==0348 (1340/3854,ALSPAC)
C==0361 (1338/3708,TWINSUK)
chr15:66598146 (GRCh38.p7) (15q22.31)
AD
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.66598146C>G
GRCh38.p7 chr 15NC_000015.10:g.66598146C>T
GRCh37.p13 chr 15NC_000015.9:g.66890484C>G
GRCh37.p13 chr 15NC_000015.9:g.66890484C>T

Gene: LINC01169, long intergenic non-protein coding RNA 1169(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01169 transcriptNR_110372.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.359G=0.641
1000GenomesAmericanSub694C=0.340G=0.660
1000GenomesEast AsianSub1008C=0.728G=0.272
1000GenomesEuropeSub1006C=0.333G=0.667
1000GenomesGlobalStudy-wide5008C=0.432G=0.568
1000GenomesSouth AsianSub978C=0.390G=0.610
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.348G=0.652
The Genome Aggregation DatabaseAfricanSub8714C=0.370G=0.629
The Genome Aggregation DatabaseAmericanSub836C=0.360G=0.64,
The Genome Aggregation DatabaseEast AsianSub1618C=0.794G=0.206
The Genome Aggregation DatabaseEuropeSub18456C=0.342G=0.657
The Genome Aggregation DatabaseGlobalStudy-wide29924C=0.377G=0.622
The Genome Aggregation DatabaseOtherSub300C=0.500G=0.50,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.365G=0.634
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.361G=0.639
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs24393530.000206alcohol dependence21314694

eQTL of rs2439353 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 rs2439353 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 )
chr157538201175382398E068-16997
chr157540728775407428E0687892
chr157540728775407428E0697892
chr157536169775361747E071-37648
chr157536190475362158E071-37237
chr157536219875362356E071-37039
chr157536241775362501E071-36894
chr157536256875362625E071-36770
chr157539698875397911E071-1484
chr157540253175402680E0713136
chr157541656375416758E07117168
chr157540728775407428E0737892
chr157540728775407428E0747892
chr157535050375350607E081-48788
chr157535065975351050E081-48345