rs7731258

Homo sapiens
G>A
LINC01033 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0171 (5125/29956,GnomAD)
A=0175 (5112/29118,TOPMED)
A=0248 (1240/5008,1000G)
A=0127 (491/3854,ALSPAC)
A=0117 (435/3708,TWINSUK)
chr5:54415292 (GRCh38.p7) (5q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
31 Enhancers around
7 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.54415292G>A
GRCh37.p13 chr 5NC_000005.9:g.53711122G>A

Gene: LINC01033, long intergenic non-protein coding RNA 1033(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
LINC01033 transcriptNR_126379.1:n.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.745A=0.255
1000GenomesAmericanSub694G=0.760A=0.240
1000GenomesEast AsianSub1008G=0.619A=0.381
1000GenomesEuropeSub1006G=0.881A=0.119
1000GenomesGlobalStudy-wide5008G=0.752A=0.248
1000GenomesSouth AsianSub978G=0.760A=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.873A=0.127
The Genome Aggregation DatabaseAfricanSub8728G=0.777A=0.223
The Genome Aggregation DatabaseAmericanSub838G=0.780A=0.220
The Genome Aggregation DatabaseEast AsianSub1612G=0.616A=0.384
The Genome Aggregation DatabaseEuropeSub18478G=0.874A=0.125
The Genome Aggregation DatabaseGlobalStudy-wide29956G=0.828A=0.171
The Genome Aggregation DatabaseOtherSub300G=0.830A=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.824A=0.175
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.883A=0.117
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
rs77312580.00051alcohol dependence20201924

eQTL of rs7731258 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 rs7731258 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 )
chr55375097353751066E06839851
chr55375113953751216E06940017
chr55375075253750827E07039630
chr55375097353751066E07039851
chr55375113953751216E07040017
chr55375287453753568E07041752
chr55373625053737123E07125128
chr55375287453753568E07141752
chr55375113953751216E07340017
chr55375126553751672E07340143
chr55368040153680543E081-30579
chr55368104453681117E081-30005
chr55368187653682133E081-28989
chr55368214453682243E081-28879
chr55368228253682505E081-28617
chr55368294553683158E081-27964
chr55368331953683489E081-27633
chr55369906853699260E081-11862
chr55369934553699559E081-11563
chr55369972953700116E081-11006
chr55370012453700273E081-10849
chr55370044053700685E081-10437
chr55374900653749130E08137884
chr55375075253750827E08139630
chr55375097353751066E08139851
chr55375113953751216E08140017
chr55375126553751672E08140143
chr55368187653682133E082-28989
chr55368214453682243E082-28879
chr55375113953751216E08240017
chr55375126553751672E08240143







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55375174953751948E06740627
chr55375174953751948E06840627
chr55375174953751948E06940627
chr55375174953751948E07040627
chr55375174953751948E07140627
chr55375174953751948E07240627
chr55375174953751948E07440627