rs1501304

Homo sapiens
T>A / T>C
SHISA9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0382 (11447/29926,GnomAD)
T==0374 (10908/29118,TOPMED)
T==0480 (2403/5008,1000G)
T==0298 (1147/3854,ALSPAC)
T==0311 (1152/3708,TWINSUK)
chr16:13050831 (GRCh38.p7) (16p13.12)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.13050831T>A
GRCh38.p7 chr 16NC_000016.10:g.13050831T>C
GRCh37.p13 chr 16NC_000016.9:g.13144688T>A
GRCh37.p13 chr 16NC_000016.9:g.13144688T>C

Gene: SHISA9, shisa family member 9(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SHISA9 transcript variant 1NM_001145204.2:c.N/AIntron Variant
SHISA9 transcript variant 2NM_001145205.1:c.N/AGenic Downstream Transcript Variant
SHISA9 transcript variant X1XM_005255539.3:c.N/AIntron Variant
SHISA9 transcript variant X2XM_011522642.2:c.N/AIntron Variant
SHISA9 transcript variant X4XR_001751975.1:n.N/AIntron Variant
SHISA9 transcript variant X4XR_001751976.1:n.N/AIntron Variant
SHISA9 transcript variant X3XR_932915.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.453C=0.547
1000GenomesAmericanSub694T=0.440C=0.560
1000GenomesEast AsianSub1008T=0.690C=0.310
1000GenomesEuropeSub1006T=0.300C=0.700
1000GenomesGlobalStudy-wide5008T=0.480C=0.520
1000GenomesSouth AsianSub978T=0.520C=0.480
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.298C=0.702
The Genome Aggregation DatabaseAfricanSub8696T=0.449A=0.000
The Genome Aggregation DatabaseAmericanSub838T=0.440A=0.00,
The Genome Aggregation DatabaseEast AsianSub1616T=0.671A=0.001
The Genome Aggregation DatabaseEuropeSub18474T=0.323A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29926T=0.382A=0.000
The Genome Aggregation DatabaseOtherSub302T=0.390A=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.374C=0.625
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.311C=0.689
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
rs15013040.00045alcohol dependence20201924

eQTL of rs1501304 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr16:13144688SHISA9ENSG00000237515.6T>C8.4728e-4149211Cerebellum

meQTL of rs1501304 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 )
chr166485407064854342E07136062
chr166485474264854899E07436734
chr166479585164795901E081-22107
chr166479618664796411E081-21597