rs6740940

Homo sapiens
C>T
LRRTM4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0344 (10289/29862,GnomAD)
C==0324 (9436/29116,TOPMED)
C==0314 (1571/5008,1000G)
C==0394 (1520/3854,ALSPAC)
C==0397 (1473/3708,TWINSUK)
chr2:77234761 (GRCh38.p7) (2p12)
CD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.77234761C>T
GRCh37.p13 chr 2NC_000002.11:g.77461887C>T

Gene: LRRTM4, leucine rich repeat transmembrane neuronal 4(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LRRTM4 transcript variant 1NM_001134745.1:c.N/AIntron Variant
LRRTM4 transcript variant 3NM_001282924.1:c.N/AIntron Variant
LRRTM4 transcript variant 4NM_001282928.1:c.N/AGenic Downstream Transcript Variant
LRRTM4 transcript variant 2NM_024993.4:c.N/AGenic Downstream Transcript Variant
LRRTM4 transcript variant X1XM_011533117.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.264T=0.736
1000GenomesAmericanSub694C=0.300T=0.700
1000GenomesEast AsianSub1008C=0.342T=0.658
1000GenomesEuropeSub1006C=0.363T=0.637
1000GenomesGlobalStudy-wide5008C=0.314T=0.686
1000GenomesSouth AsianSub978C=0.310T=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.394T=0.606
The Genome Aggregation DatabaseAfricanSub8682C=0.279T=0.721
The Genome Aggregation DatabaseAmericanSub834C=0.310T=0.690
The Genome Aggregation DatabaseEast AsianSub1600C=0.330T=0.670
The Genome Aggregation DatabaseEuropeSub18444C=0.377T=0.622
The Genome Aggregation DatabaseGlobalStudy-wide29862C=0.344T=0.655
The Genome Aggregation DatabaseOtherSub302C=0.400T=0.600
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.324T=0.675
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.397T=0.603
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
rs67409402.95E-05cocaine dependence23958962

eQTL of rs6740940 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 rs6740940 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 )
chr27745564777455915E070-5972
chr27745603977456217E070-5670
chr27745564777455915E081-5972
chr27745603977456217E081-5670
chr27745564777455915E082-5972
chr27745603977456217E082-5670