rs702354

Homo sapiens
T>C
SAMD5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0271 (8108/29836,GnomAD)
T==0238 (6956/29118,TOPMED)
T==0219 (1098/5008,1000G)
T==0339 (1305/3854,ALSPAC)
T==0341 (1266/3708,TWINSUK)
chr6:147601419 (GRCh38.p7) (6q24.3)
ND
GWASdb2
1   publication(s)
See rs on genome
20 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.147601419T>C
GRCh37.p13 chr 6NC_000006.11:g.147922555T>C

Gene: SAMD5, sterile alpha motif domain containing 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SAMD5 transcriptNM_001030060.2:c.N/AGenic Downstream Transcript Variant
SAMD5 transcript variant X1XM_017010850.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.126C=0.874
1000GenomesAmericanSub694T=0.210C=0.790
1000GenomesEast AsianSub1008T=0.225C=0.775
1000GenomesEuropeSub1006T=0.336C=0.664
1000GenomesGlobalStudy-wide5008T=0.219C=0.781
1000GenomesSouth AsianSub978T=0.230C=0.770
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.339C=0.661
The Genome Aggregation DatabaseAfricanSub8690T=0.159C=0.841
The Genome Aggregation DatabaseAmericanSub832T=0.200C=0.800
The Genome Aggregation DatabaseEast AsianSub1610T=0.225C=0.775
The Genome Aggregation DatabaseEuropeSub18402T=0.330C=0.669
The Genome Aggregation DatabaseGlobalStudy-wide29836T=0.271C=0.728
The Genome Aggregation DatabaseOtherSub302T=0.390C=0.610
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.238C=0.761
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.341C=0.659
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs7023540.000173nicotine dependence17158188

eQTL of rs702354 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 rs702354 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 )
chr6147879754147879872E070-42683
chr6147879997147880778E070-41777
chr6147924633147924823E0702078
chr6147925107147925157E0702552
chr6147905560147905612E081-16943
chr6147906542147906626E081-15929
chr6147906709147906804E081-15751
chr6147906955147907730E081-14825
chr6147908923147909155E081-13400
chr6147909176147909313E081-13242
chr6147909700147909794E081-12761
chr6147910140147910190E081-12365
chr6147910489147911493E081-11062
chr6147922652147922740E08197
chr6147922751147922821E081196
chr6147922876147923316E081321
chr6147906542147906626E082-15929
chr6147906709147906804E082-15751
chr6147906955147907730E082-14825
chr6147910489147911493E082-11062