rs1004064

Homo sapiens
G>A
LINC01258 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0086 (2593/29910,GnomAD)
A=0108 (3144/29118,TOPMED)
A=0142 (712/5008,1000G)
A=0065 (252/3854,ALSPAC)
A=0059 (218/3708,TWINSUK)
chr4:38456999 (GRCh38.p7) (4p14)
AD
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.38456999G>A
GRCh37.p13 chr 4NC_000004.11:g.38458620G>A

Gene: LINC01258, long intergenic non-protein coding RNA 1258(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01258 transcriptNR_110951.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.820A=0.180
1000GenomesAmericanSub694G=0.900A=0.100
1000GenomesEast AsianSub1008G=0.983A=0.017
1000GenomesEuropeSub1006G=0.939A=0.061
1000GenomesGlobalStudy-wide5008G=0.858A=0.142
1000GenomesSouth AsianSub978G=0.660A=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.935A=0.065
The Genome Aggregation DatabaseAfricanSub8688G=0.849A=0.151
The Genome Aggregation DatabaseAmericanSub836G=0.930A=0.070
The Genome Aggregation DatabaseEast AsianSub1622G=0.993A=0.007
The Genome Aggregation DatabaseEuropeSub18462G=0.936A=0.063
The Genome Aggregation DatabaseGlobalStudy-wide29910G=0.913A=0.086
The Genome Aggregation DatabaseOtherSub302G=0.900A=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.892A=0.108
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.941A=0.059
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs10040648.5E-05alcoholism (heaviness of drinking)21529783

eQTL of rs1004064 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 rs1004064 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 )
chr43849058438492286E06731964
chr43842597238426242E068-32378
chr43842625638426492E068-32128
chr43849247638492544E06833856
chr43849277438493023E06834154
chr43849896838499141E06840348
chr43849058438492286E06931964
chr43849058438492286E07131964
chr43849247638492544E07133856
chr43849277438493023E07134154
chr43849058438492286E07231964
chr43849247638492544E07233856
chr43849277438493023E07234154
chr43849058438492286E07331964
chr43849247638492544E07333856
chr43849058438492286E07431964
chr43849247638492544E07433856
chr43849277438493023E07434154
chr43849896838499141E07440348