rs13259289

Homo sapiens
T>C
CSMD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0297 (8912/29956,GnomAD)
C=0260 (7583/29118,TOPMED)
C=0159 (794/5008,1000G)
C=0401 (1547/3854,ALSPAC)
C=0394 (1460/3708,TWINSUK)
chr8:4252510 (GRCh38.p7) (8p23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
26 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.4252510T>C
GRCh37.p13 chr 8NC_000008.10:g.4110032T>C

Gene: CSMD1, CUB and Sushi multiple domains 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CSMD1 transcriptNM_033225.5:c.N/AIntron Variant
CSMD1 transcript variant X1XM_011534752.2:c.N/AIntron Variant
CSMD1 transcript variant X2XM_017013731.1:c.N/AIntron Variant
CSMD1 transcript variant X3XM_011534753.2:c.N/AGenic Upstream Transcript Variant
CSMD1 transcript variant X4XM_011534754.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.925C=0.075
1000GenomesAmericanSub694T=0.710C=0.290
1000GenomesEast AsianSub1008T=0.996C=0.004
1000GenomesEuropeSub1006T=0.590C=0.410
1000GenomesGlobalStudy-wide5008T=0.841C=0.159
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.599C=0.401
The Genome Aggregation DatabaseAfricanSub8726T=0.888C=0.112
The Genome Aggregation DatabaseAmericanSub838T=0.690C=0.310
The Genome Aggregation DatabaseEast AsianSub1622T=0.998C=0.002
The Genome Aggregation DatabaseEuropeSub18468T=0.591C=0.409
The Genome Aggregation DatabaseGlobalStudy-wide29956T=0.702C=0.297
The Genome Aggregation DatabaseOtherSub302T=0.610C=0.390
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.739C=0.260
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.606C=0.394
PMID Title Author Journal
23942779A genome-wide association study of behavioral disinhibition.McGue MBehav Genet

P-Value

SNP ID p-value Traits Study
rs132592890.00022alcohol consumption23942779
rs132592890.00053alcohol dependence23942779

eQTL of rs13259289 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 rs13259289 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 )
chr840723464072970E070-37062
chr840732894073339E070-36693
chr840721864072236E072-37796
chr840723464072970E072-37062
chr840706974070910E081-39122
chr840709474071270E081-38762
chr840721864072236E081-37796
chr840723464072970E081-37062
chr840732894073339E081-36693
chr840734494073801E081-36231
chr840738374073936E081-36096
chr840740954074183E081-35849
chr840744034074453E081-35579
chr841469534147081E08136921
chr841470934147266E08137061
chr841477324147805E08137700
chr840709474071270E082-38762
chr840723464072970E082-37062
chr840732894073339E082-36693
chr840734494073801E082-36231
chr840738374073936E082-36096
chr840740954074183E082-35849
chr841393854139435E08229353
chr841395144139597E08229482
chr841399784140028E08229946
chr841477324147805E08237700