rs954237

Homo sapiens
T>C
SCGB1D4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0357 (10687/29918,GnomAD)
T==0365 (10651/29116,TOPMED)
T==0291 (1455/5008,1000G)
T==0331 (1274/3854,ALSPAC)
T==0327 (1213/3708,TWINSUK)
chr11:62297243 (GRCh38.p7) (11q12.3)
CD
GWASdb2
1   publication(s)
See rs on genome
71 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.62297243T>C
GRCh37.p13 chr 11NC_000011.9:g.62064715T>C

Gene: SCGB1D4, secretoglobin family 1D member 4(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SCGB1D4 transcriptNM_206998.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.438C=0.562
1000GenomesAmericanSub694T=0.220C=0.780
1000GenomesEast AsianSub1008T=0.197C=0.803
1000GenomesEuropeSub1006T=0.328C=0.672
1000GenomesGlobalStudy-wide5008T=0.291C=0.709
1000GenomesSouth AsianSub978T=0.200C=0.800
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.331C=0.669
The Genome Aggregation DatabaseAfricanSub8700T=0.412C=0.588
The Genome Aggregation DatabaseAmericanSub838T=0.190C=0.810
The Genome Aggregation DatabaseEast AsianSub1614T=0.186C=0.814
The Genome Aggregation DatabaseEuropeSub18464T=0.354C=0.645
The Genome Aggregation DatabaseGlobalStudy-wide29918T=0.357C=0.642
The Genome Aggregation DatabaseOtherSub302T=0.320C=0.680
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.365C=0.634
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.327C=0.673
PMID Title Author Journal
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs9542370.0000105cocaine dependence(EA)23958962
rs9542370.000138cocaine dependence(ALL)23958962

eQTL of rs954237 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 rs954237 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 )
chr116210417762104240E06739462
chr116210433662104386E06739621
chr116210446062104500E06739745
chr116210761662107690E06742901
chr116210772362108080E06743008
chr116210816762108311E06743452
chr116210651662106671E06841801
chr116210668962106918E06841974
chr116210693162107047E06842216
chr116210718162107267E06842466
chr116210727162107600E06842556
chr116210772362108080E06843008
chr116210816762108311E06843452
chr116210693162107047E06942216
chr116210718162107267E06942466
chr116210727162107600E06942556
chr116210761662107690E06942901
chr116210651662106671E07041801
chr116210668962106918E07041974
chr116210693162107047E07042216
chr116210718162107267E07042466
chr116210727162107600E07042556
chr116210761662107690E07042901
chr116210816762108311E07043452
chr116210651662106671E07141801
chr116210668962106918E07141974
chr116210693162107047E07142216
chr116210718162107267E07142466
chr116210727162107600E07142556
chr116210761662107690E07142901
chr116210772362108080E07143008
chr116210816762108311E07143452
chr116210417762104240E07239462
chr116210433662104386E07239621
chr116210651662106671E07341801
chr116210668962106918E07341974
chr116210693162107047E07342216
chr116210718162107267E07342466
chr116210727162107600E07342556
chr116210761662107690E07342901
chr116210772362108080E07343008
chr116210816762108311E07343452
chr116210417762104240E07439462
chr116210433662104386E07439621
chr116210446062104500E07439745
chr116210651662106671E07441801
chr116210668962106918E07441974
chr116210693162107047E07442216
chr116210718162107267E07442466
chr116210727162107600E07442556
chr116210761662107690E07442901
chr116210772362108080E07443008
chr116210816762108311E07443452
chr116210417762104240E08139462
chr116210433662104386E08139621
chr116210446062104500E08139745
chr116210651662106671E08141801
chr116210668962106918E08141974
chr116210693162107047E08142216
chr116210718162107267E08142466
chr116210727162107600E08142556
chr116210761662107690E08142901
chr116210772362108080E08143008
chr116210816762108311E08143452
chr116210651662106671E08241801
chr116210668962106918E08241974
chr116210693162107047E08242216
chr116210718162107267E08242466
chr116210727162107600E08242556
chr116210761662107690E08242901
chr116210772362108080E08243008










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr116210463562105705E06739920
chr116210578362105940E06741068
chr116210463562105705E06839920
chr116210578362105940E06841068
chr116210463562105705E06939920
chr116210578362105940E06941068
chr116210463562105705E07039920
chr116210578362105940E07041068
chr116210463562105705E07139920
chr116210578362105940E07141068
chr116210463562105705E07239920
chr116210578362105940E07241068
chr116210463562105705E07339920
chr116210578362105940E07341068
chr116210463562105705E07439920
chr116210578362105940E07441068
chr116210463562105705E08139920
chr116210578362105940E08141068
chr116210463562105705E08239920
chr116210578362105940E08241068