rs7448080

Homo sapiens
T>C
LINC01170 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0072 (2158/29960,GnomAD)
T==0091 (2657/29118,TOPMED)
T==0107 (534/5008,1000G)
T==0056 (217/3854,ALSPAC)
T==0065 (240/3708,TWINSUK)
chr5:124062405 (GRCh38.p7) (5q23.2)
AD
GWASdb2 | GWASCatalog
1   publication(s)
See rs on genome
54 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.124062405T>C
GRCh37.p13 chr 5NC_000005.9:g.123398098T>C

Gene: LINC01170, long intergenic non-protein coding RNA 1170(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01170 transcriptNR_125774.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.152C=0.848
1000GenomesAmericanSub694T=0.070C=0.930
1000GenomesEast AsianSub1008T=0.106C=0.894
1000GenomesEuropeSub1006T=0.055C=0.945
1000GenomesGlobalStudy-wide5008T=0.107C=0.893
1000GenomesSouth AsianSub978T=0.120C=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.056C=0.944
The Genome Aggregation DatabaseAfricanSub8726T=0.113C=0.887
The Genome Aggregation DatabaseAmericanSub838T=0.090C=0.910
The Genome Aggregation DatabaseEast AsianSub1594T=0.110C=0.890
The Genome Aggregation DatabaseEuropeSub18500T=0.047C=0.952
The Genome Aggregation DatabaseGlobalStudy-wide29960T=0.072C=0.928
The Genome Aggregation DatabaseOtherSub302T=0.130C=0.870
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.091C=0.908
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.065C=0.935
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs74480804E-06alcohol dependence (age at onset)24962325

eQTL of rs7448080 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 rs7448080 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 )
chr5123365705123366284E067-31814
chr5123391122123391193E067-6905
chr5123392125123393946E067-4152
chr5123375194123375468E068-22630
chr5123375511123375689E068-22409
chr5123396762123397029E068-1069
chr5123397324123397434E068-664
chr5123397463123397677E068-421
chr5123365705123366284E069-31814
chr5123365705123366284E070-31814
chr5123380311123380637E070-17461
chr5123392125123393946E070-4152
chr5123395536123395576E070-2522
chr5123396243123396311E070-1787
chr5123396495123396711E070-1387
chr5123396762123397029E070-1069
chr5123397463123397677E070-421
chr5123397902123397960E070-138
chr5123424172123424223E07026074
chr5123365705123366284E071-31814
chr5123391122123391193E071-6905
chr5123397324123397434E071-664
chr5123397463123397677E071-421
chr5123365705123366284E072-31814
chr5123365705123366284E074-31814
chr5123385415123385624E074-12474
chr5123385883123386085E074-12013
chr5123424172123424223E07426074
chr5123361092123361406E081-36692
chr5123361557123361784E081-36314
chr5123365705123366284E081-31814
chr5123374493123374556E081-23542
chr5123392125123393946E081-4152
chr5123395904123395966E081-2132
chr5123396243123396311E081-1787
chr5123396495123396711E081-1387
chr5123396762123397029E081-1069
chr5123397324123397434E081-664
chr5123397463123397677E081-421
chr5123397902123397960E081-138
chr5123424172123424223E08126074
chr5123361092123361406E082-36692
chr5123365705123366284E082-31814
chr5123375194123375468E082-22630
chr5123375511123375689E082-22409
chr5123381208123381375E082-16723
chr5123392125123393946E082-4152
chr5123395904123395966E082-2132
chr5123396243123396311E082-1787
chr5123396495123396711E082-1387
chr5123396762123397029E082-1069
chr5123397324123397434E082-664
chr5123397463123397677E082-421
chr5123397902123397960E082-138