rs2305024

Homo sapiens
A>C
TTC39C : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0174 (5239/29950,GnomAD)
A==0229 (6690/29118,TOPMED)
A==0247 (1235/5008,1000G)
A==0062 (239/3854,ALSPAC)
A==0066 (243/3708,TWINSUK)
chr18:24082852 (GRCh38.p7) (18q11.2)
ND
GWASdb2
1   publication(s)
See rs on genome
30 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.24082852A>C
GRCh37.p13 chr 18NC_000018.9:g.21662816A>C

Gene: TTC39C, tetratricopeptide repeat domain 39C(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TTC39C transcript variant 1NM_001135993.1:c.N/AIntron Variant
TTC39C transcript variant 2NM_153211.3:c.N/AIntron Variant
TTC39C transcript variant 4NM_001292030.1:c.N/AGenic Upstream Transcript Variant
TTC39C transcript variant 3NM_001243425.1:c.N/AGenic Downstream Transcript Variant
TTC39C transcript variant X2XM_005258198.4:c.N/AIntron Variant
TTC39C transcript variant X4XM_006722392.3:c.N/AIntron Variant
TTC39C transcript variant X1XM_011525814.2:c.N/AIntron Variant
TTC39C transcript variant X3XM_017025550.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.512C=0.488
1000GenomesAmericanSub694A=0.060C=0.940
1000GenomesEast AsianSub1008A=0.216C=0.784
1000GenomesEuropeSub1006A=0.057C=0.943
1000GenomesGlobalStudy-wide5008A=0.247C=0.753
1000GenomesSouth AsianSub978A=0.240C=0.760
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.062C=0.938
The Genome Aggregation DatabaseAfricanSub8696A=0.431C=0.569
The Genome Aggregation DatabaseAmericanSub836A=0.060C=0.940
The Genome Aggregation DatabaseEast AsianSub1618A=0.230C=0.770
The Genome Aggregation DatabaseEuropeSub18498A=0.056C=0.943
The Genome Aggregation DatabaseGlobalStudy-wide29950A=0.174C=0.825
The Genome Aggregation DatabaseOtherSub302A=0.070C=0.930
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.229C=0.770
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.066C=0.934
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs23050242.05E-05alcohol and nictotine co-dependence20158304

eQTL of rs2305024 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 rs2305024 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 )
chr182163400921634576E067-28240
chr182164220821642407E067-20409
chr182166861421668675E0675798
chr182166881521668954E0675999
chr182166899821669604E0676182
chr182163348921633685E068-29131
chr182163381721633913E068-28903
chr182163400921634576E068-28240
chr182163320321633395E069-29421
chr182163348921633685E069-29131
chr182163381721633913E069-28903
chr182163400921634576E069-28240
chr182166881521668954E0695999
chr182166899821669604E0696182
chr182163348921633685E071-29131
chr182163381721633913E071-28903
chr182163400921634576E071-28240
chr182166665521666760E0723839
chr182166861421668675E0725798
chr182166881521668954E0725999
chr182166899821669604E0726182
chr182166833521668512E0735519
chr182166861421668675E0735798
chr182166881521668954E0735999
chr182166899821669604E0736182
chr182168445021684501E08121634
chr182168452221684603E08121706
chr182168724821687323E08124432
chr182168737721687501E08124561
chr182164613921646471E082-16345