rs17729321

Homo sapiens
T>C
LOC105377684 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0027 (836/29966,GnomAD)
C=0026 (765/29118,TOPMED)
C=0019 (95/5008,1000G)
C=0049 (187/3854,ALSPAC)
C=0042 (154/3708,TWINSUK)
chr5:159560721 (GRCh38.p7) (5q33.3)
ND
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.159560721T>C
GRCh37.p13 chr 5NC_000005.9:g.158987729T>C

Gene: LOC105377684, uncharacterized LOC105377684(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377684 transcript variant X1XR_941139.2:n.N/AIntron Variant
LOC105377684 transcript variant X2XR_941141.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.996C=0.004
1000GenomesAmericanSub694T=0.960C=0.040
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.957C=0.043
1000GenomesGlobalStudy-wide5008T=0.981C=0.019
1000GenomesSouth AsianSub978T=0.980C=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.951C=0.049
The Genome Aggregation DatabaseAfricanSub8728T=0.994C=0.006
The Genome Aggregation DatabaseAmericanSub838T=0.970C=0.030
The Genome Aggregation DatabaseEast AsianSub1606T=0.999C=0.001
The Genome Aggregation DatabaseEuropeSub18492T=0.959C=0.040
The Genome Aggregation DatabaseGlobalStudy-wide29966T=0.972C=0.027
The Genome Aggregation DatabaseOtherSub302T=0.980C=0.020
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.973C=0.026
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.958C=0.042
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
rs177293214.17E-05alcohol and nictotine co-dependence20158304

eQTL of rs17729321 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 rs17729321 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 )
chr5158952173158952410E081-35319
chr5158952432158952545E081-35184
chr5158992648158992705E0814919
chr5158993736158994665E0816007
chr5158992648158992705E0824919
chr5158993736158994665E0826007