rs16994074

Homo sapiens
T>C
TBC1D1 : Intron Variant
LOC105374407 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0159 (4777/29970,GnomAD)
C=0150 (4378/29118,TOPMED)
C=0116 (581/5008,1000G)
C=0156 (602/3854,ALSPAC)
C=0151 (559/3708,TWINSUK)
chr4:37924357 (GRCh38.p7) (4p14)
CD
GWASdb2
1   publication(s)
See rs on genome
37 Enhancers around
43 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.37924357T>C
GRCh37.p13 chr 4NC_000004.11:g.37925978T>C

Gene: TBC1D1, TBC1 domain family member 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TBC1D1 transcript variant 2NM_001253912.1:c.N/AIntron Variant
TBC1D1 transcript variant 1NM_015173.3:c.N/AIntron Variant
TBC1D1 transcript variant 3NM_001253913.1:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant 4NM_001253914.1:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant 5NM_001253915.1:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant X3XM_005262646.2:c.N/AIntron Variant
TBC1D1 transcript variant X4XM_005262647.2:c.N/AIntron Variant
TBC1D1 transcript variant X1XM_011513659.2:c.N/AIntron Variant
TBC1D1 transcript variant X2XM_011513660.2:c.N/AIntron Variant
TBC1D1 transcript variant X5XM_011513662.2:c.N/AIntron Variant
TBC1D1 transcript variant X6XM_011513663.2:c.N/AIntron Variant
TBC1D1 transcript variant X7XM_011513664.2:c.N/AIntron Variant
TBC1D1 transcript variant X10XM_011513665.2:c.N/AIntron Variant
TBC1D1 transcript variant X11XM_011513666.2:c.N/AIntron Variant
TBC1D1 transcript variant X17XM_011513668.2:c.N/AIntron Variant
TBC1D1 transcript variant X8XM_017007918.1:c.N/AIntron Variant
TBC1D1 transcript variant X9XM_017007919.1:c.N/AIntron Variant
TBC1D1 transcript variant X12XM_017007920.1:c.N/AIntron Variant
TBC1D1 transcript variant X15XM_017007922.1:c.N/AIntron Variant
TBC1D1 transcript variant X13XM_005262649.2:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant X18XM_006714001.2:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant X19XM_011513670.2:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant X14XM_017007921.1:c.N/AGenic Upstream Transcript Variant
TBC1D1 transcript variant X16XR_001741181.1:n.N/AIntron Variant

Gene: LOC105374407, uncharacterized LOC105374407(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105374407 transcriptXR_925212.2:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.860C=0.140
1000GenomesAmericanSub694T=0.900C=0.100
1000GenomesEast AsianSub1008T=0.943C=0.057
1000GenomesEuropeSub1006T=0.833C=0.167
1000GenomesGlobalStudy-wide5008T=0.884C=0.116
1000GenomesSouth AsianSub978T=0.900C=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.844C=0.156
The Genome Aggregation DatabaseAfricanSub8724T=0.849C=0.151
The Genome Aggregation DatabaseAmericanSub836T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1622T=0.960C=0.040
The Genome Aggregation DatabaseEuropeSub18486T=0.823C=0.177
The Genome Aggregation DatabaseGlobalStudy-wide29970T=0.840C=0.159
The Genome Aggregation DatabaseOtherSub302T=0.830C=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.849C=0.150
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.849C=0.151
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
rs169940745.41E-05cocaine dependence23958962

eQTL of rs16994074 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 rs16994074 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 )
chr43789825637898316E068-27662
chr43791177937911991E068-13987
chr43793808137938219E06812103
chr43793839837938456E06812420
chr43793857137938836E06812593
chr43789099837891139E069-34839
chr43792991437929981E0693936
chr43793009937930554E0694121
chr43793058437930828E0694606
chr43791011437910688E070-15290
chr43791076337910835E070-15143
chr43792662837926883E070650
chr43792911037929319E0703132
chr43792991437929981E0703936
chr43793009937930554E0704121
chr43793058437930828E0704606
chr43789825637898316E071-27662
chr43791011437910688E071-15290
chr43791076337910835E071-15143
chr43789099837891139E072-34839
chr43789825637898316E074-27662
chr43791011437910688E081-15290
chr43791103737911188E081-14790
chr43791921237919256E081-6722
chr43791977537919892E081-6086
chr43792039537920445E081-5533
chr43792049237920564E081-5414
chr43792118137921291E081-4687
chr43792137637921445E081-4533
chr43792911037929319E0813132
chr43792991437929981E0813936
chr43793009937930554E0814121
chr43793058437930828E0814606
chr43792911037929319E0823132
chr43792991437929981E0823936
chr43793058437930828E0824606
chr43793361337933855E0827635








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr43789121037891263E067-34715
chr43789127937891328E067-34650
chr43789136437891437E067-34541
chr43789146437893701E067-32277
chr43789373837893902E067-32076
chr43789121037891263E068-34715
chr43789127937891328E068-34650
chr43789136437891437E068-34541
chr43789146437893701E068-32277
chr43789121037891263E069-34715
chr43789127937891328E069-34650
chr43789136437891437E069-34541
chr43789146437893701E069-32277
chr43789373837893902E069-32076
chr43789146437893701E070-32277
chr43789121037891263E071-34715
chr43789127937891328E071-34650
chr43789136437891437E071-34541
chr43789146437893701E071-32277
chr43789373837893902E071-32076
chr43789121037891263E072-34715
chr43789127937891328E072-34650
chr43789136437891437E072-34541
chr43789146437893701E072-32277
chr43789373837893902E072-32076
chr43789121037891263E073-34715
chr43789127937891328E073-34650
chr43789136437891437E073-34541
chr43789146437893701E073-32277
chr43789373837893902E073-32076
chr43789121037891263E074-34715
chr43789127937891328E074-34650
chr43789136437891437E074-34541
chr43789146437893701E074-32277
chr43789373837893902E074-32076
chr43789136437891437E081-34541
chr43789146437893701E081-32277
chr43789373837893902E081-32076
chr43789121037891263E082-34715
chr43789127937891328E082-34650
chr43789136437891437E082-34541
chr43789146437893701E082-32277
chr43789373837893902E082-32076