rs844562

Homo sapiens
T>C
SAMD5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0405 (12141/29920,GnomAD)
T==0380 (11074/29118,TOPMED)
T==0430 (2151/5008,1000G)
T==0416 (1602/3854,ALSPAC)
T==0415 (1539/3708,TWINSUK)
chr6:147587859 (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.147587859T>C
GRCh37.p13 chr 6NC_000006.11:g.147908995T>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=0.346C=0.654
1000GenomesAmericanSub694T=0.400C=0.600
1000GenomesEast AsianSub1008T=0.540C=0.460
1000GenomesEuropeSub1006T=0.404C=0.596
1000GenomesGlobalStudy-wide5008T=0.430C=0.570
1000GenomesSouth AsianSub978T=0.470C=0.530
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.416C=0.584
The Genome Aggregation DatabaseAfricanSub8706T=0.358C=0.642
The Genome Aggregation DatabaseAmericanSub836T=0.380C=0.620
The Genome Aggregation DatabaseEast AsianSub1614T=0.571C=0.429
The Genome Aggregation DatabaseEuropeSub18462T=0.413C=0.586
The Genome Aggregation DatabaseGlobalStudy-wide29920T=0.405C=0.594
The Genome Aggregation DatabaseOtherSub302T=0.480C=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.380C=0.619
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.415C=0.585
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
rs8445620.000714nicotine dependence17158188

eQTL of rs844562 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 rs844562 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 )
chr6147879754147879872E070-29123
chr6147879997147880778E070-28217
chr6147924633147924823E07015638
chr6147925107147925157E07016112
chr6147905560147905612E081-3383
chr6147906542147906626E081-2369
chr6147906709147906804E081-2191
chr6147906955147907730E081-1265
chr6147908923147909155E0810
chr6147909176147909313E081181
chr6147909700147909794E081705
chr6147910140147910190E0811145
chr6147910489147911493E0811494
chr6147922652147922740E08113657
chr6147922751147922821E08113756
chr6147922876147923316E08113881
chr6147906542147906626E082-2369
chr6147906709147906804E082-2191
chr6147906955147907730E082-1265
chr6147910489147911493E0821494