rs547301762

Homo sapiens
dupTGCT
LINC00158 : Intron Variant
Check p-value
Indel (Insertion and Deletion)
dupTGCT=0001 (31/29118,TOPMED)
dupTGCT=0001 (4/5008,1000G)
chr21:25413996-25413999 (GRCh38.p7) (21q21.2)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.25413996_25413999dup
GRCh37.p13 chr 21NC_000021.8:g.26786308_26786311dup

Gene: LINC00158, long intergenic non-protein coding RNA 158(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00158 transcriptNR_024027.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub2416TGCT=0.453dupTGCT=0.002
1000GenomesAmericanSub1160TGCT=0.402dupTGCT=0.000
1000GenomesEast AsianSub1857TGCT=0.457dupTGCT=0.000
1000GenomesEuropeSub1477TGCT=0.319dupTGCT=0.000
1000GenomesGlobalStudy-wide5008TGCT=0.702dupTGCT=0.001
1000GenomesSouth AsianSub1616TGCT=0.395dupTGCT=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118TGCT=0.998dupTGCT=0.001
PMID Title Author Journal
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs5473017622.5E-07alcohol and nictotine co-dependence22488850

eQTL of rs547301762 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 rs547301762 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.