rs1493652

Homo sapiens
T>C
LINS1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0143 (4300/29970,GnomAD)
T==0147 (4289/29118,TOPMED)
T==0249 (1249/5008,1000G)
T==0090 (345/3854,ALSPAC)
T==0091 (339/3708,TWINSUK)
chr15:100572137 (GRCh38.p7) (15q26.3)
AD
GWASdb2
1   publication(s)
See rs on genome
34 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.100572137T>C
GRCh37.p13 chr 15NC_000015.9:g.101112342T>C
LINS1 RefSeqGeneNG_034076.1:g.35104A>G

Gene: LINS1, lines homolog 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINS1 transcript variant 1NM_001040616.2:c.N/AIntron Variant
LINS1 transcript variant X1XM_005254941.1:c.N/AIntron Variant
LINS1 transcript variant X2XM_005254943.1:c.N/AIntron Variant
LINS1 transcript variant X3XM_017022398.1:c.N/AIntron Variant
LINS1 transcript variant X4XM_017022399.1:c.N/AIntron Variant
LINS1 transcript variant X7XM_017022400.1:c.N/AIntron Variant
LINS1 transcript variant X12XR_429464.3:n.255...XR_429464.3:n.2557A>GA>GNon Coding Transcript Variant
LINS1 transcript variant X5XR_001751346.1:n.N/AIntron Variant
LINS1 transcript variant X9XR_001751347.1:n.N/AIntron Variant
LINS1 transcript variant X11XR_001751348.1:n.N/AIntron Variant
LINS1 transcript variant X10XR_243210.3:n.N/AIntron Variant
LINS1 transcript variant X6XR_931862.2:n.N/AIntron Variant
LINS1 transcript variant X8XR_931863.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.187C=0.813
1000GenomesAmericanSub694T=0.220C=0.780
1000GenomesEast AsianSub1008T=0.611C=0.389
1000GenomesEuropeSub1006T=0.087C=0.913
1000GenomesGlobalStudy-wide5008T=0.249C=0.751
1000GenomesSouth AsianSub978T=0.150C=0.850
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.090C=0.910
The Genome Aggregation DatabaseAfricanSub8728T=0.162C=0.838
The Genome Aggregation DatabaseAmericanSub836T=0.190C=0.810
The Genome Aggregation DatabaseEast AsianSub1612T=0.671C=0.329
The Genome Aggregation DatabaseEuropeSub18492T=0.084C=0.915
The Genome Aggregation DatabaseGlobalStudy-wide29970T=0.143C=0.856
The Genome Aggregation DatabaseOtherSub302T=0.250C=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.147C=0.852
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.091C=0.909
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
rs14936520.0008alcohol dependence20201924

eQTL of rs1493652 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:101112342CERS3ENSG00000154227.9T>C6.3302e-1127142Cerebellum
Chr15:101112342CERS3ENSG00000154227.9T>C1.4305e-927142Cerebellar_Hemisphere

meQTL of rs1493652 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 )
chr15101144841101144895E06732499
chr15101144965101145043E06732623
chr15101065746101066988E068-45354
chr15101140459101140499E06828117
chr15101140537101140587E06828195
chr15101140873101140917E06828531
chr15101065746101066988E069-45354
chr15101140459101140499E06928117
chr15101140537101140587E06928195
chr15101140873101140917E06928531
chr15101065241101065501E070-46841
chr15101065600101065685E070-46657
chr15101065746101066988E070-45354
chr15101071519101071674E070-40668
chr15101072034101072084E070-40258
chr15101072273101072561E070-39781
chr15101138928101139055E07026586
chr15101139098101139323E07026756
chr15101065746101066988E071-45354
chr15101139098101139323E07126756
chr15101065746101066988E072-45354
chr15101102583101102693E072-9649
chr15101140873101140917E07228531
chr15101065746101066988E074-45354
chr15101065241101065501E081-46841
chr15101065600101065685E081-46657
chr15101065746101066988E081-45354
chr15101070215101070505E081-41837
chr15101140873101140917E08128531
chr15101065746101066988E082-45354
chr15101070215101070505E082-41837
chr15101072034101072084E082-40258
chr15101072273101072561E082-39781
chr15101140873101140917E08228531









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr15101141028101143692E06728686
chr15101141028101143692E06828686
chr15101141028101143692E06928686
chr15101141028101143692E07028686
chr15101141028101143692E07128686
chr15101141028101143692E07228686
chr15101141028101143692E07328686
chr15101141028101143692E07428686
chr15101141028101143692E08128686
chr15101141028101143692E08228686