rs2589293

Homo sapiens
C>G
CSMD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0017 (526/29996,GnomAD)
C==0024 (724/29118,TOPMED)
C==0020 (100/5008,1000G)
C==0000 (1/3854,ALSPAC)
C==0000 (1/3708,TWINSUK)
chr8:3339921 (GRCh38.p7) (8p23.2)
ND
GWASdb2
1   publication(s)
See rs on genome
7 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.3339921C>G
GRCh37.p13 chr 8NC_000008.10:g.3197443C>G

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 X3XM_011534753.2:c.N/AIntron Variant
CSMD1 transcript variant X2XM_017013731.1:c.N/AIntron Variant
CSMD1 transcript variant X4XM_011534754.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.070G=0.930
1000GenomesAmericanSub694C=0.010G=0.990
1000GenomesEast AsianSub1008C=0.000G=1.000
1000GenomesEuropeSub1006C=0.001G=0.999
1000GenomesGlobalStudy-wide5008C=0.020G=0.980
1000GenomesSouth AsianSub978C=0.000G=1.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.000G=1.000
The Genome Aggregation DatabaseAfricanSub8732C=0.060G=0.940
The Genome Aggregation DatabaseAmericanSub838C=0.000G=1.000
The Genome Aggregation DatabaseEast AsianSub1622C=0.000G=1.000
The Genome Aggregation DatabaseEuropeSub18502C=0.000G=0.999
The Genome Aggregation DatabaseGlobalStudy-wide29996C=0.017G=0.982
The Genome Aggregation DatabaseOtherSub302C=0.000G=1.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.024G=0.975
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.000G=1.000
PMID Title Author Journal
17407593Molecular genetics of nicotine dependence and abstinence: whole genome association using 520,000 SNPs.Uhl GRBMC Genet

P-Value

SNP ID p-value Traits Study
rs25892930.00083nicotine dependence17407593

eQTL of rs2589293 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 rs2589293 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 )
chr831923433192464E074-4979
chr831925253192590E074-4853
chr831678893167939E081-29504
chr831682563168319E081-29124
chr831786953178735E081-18708
chr831789083178958E081-18485
chr831789773179303E081-18140


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr832159543216449E06718511
chr832159543216449E06818511
chr832159543216449E07118511
chr832159543216449E07418511