SNP Detail Info-rs844562

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SAMD5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

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)

Position: chr6:147587859 (GRCh38.p7) (6q24.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 20 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.147587859T>C
GRCh37.p13 chr 6	NC_000006.11:g.147908995T>C

Molecule type	Change	Amino acid[Codon]	SO Term
SAMD5 transcript	NM_001030060.2:c.	N/A	Genic Downstream Transcript Variant
SAMD5 transcript variant X1	XM_017010850.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.346	C=0.654
1000Genomes	American	Sub	694	T=0.400	C=0.600
1000Genomes	East Asian	Sub	1008	T=0.540	C=0.460
1000Genomes	Europe	Sub	1006	T=0.404	C=0.596
1000Genomes	Global	Study-wide	5008	T=0.430	C=0.570
1000Genomes	South Asian	Sub	978	T=0.470	C=0.530
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.416	C=0.584
The Genome Aggregation Database	African	Sub	8706	T=0.358	C=0.642
The Genome Aggregation Database	American	Sub	836	T=0.380	C=0.620
The Genome Aggregation Database	East Asian	Sub	1614	T=0.571	C=0.429
The Genome Aggregation Database	Europe	Sub	18462	T=0.413	C=0.586
The Genome Aggregation Database	Global	Study-wide	29920	T=0.405	C=0.594
The Genome Aggregation Database	Other	Sub	302	T=0.480	C=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.380	C=0.619
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.415	C=0.585

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

SNP ID	p-value	Traits	Study
rs844562	0.000714	nicotine dependence	17158188

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr6	147879754	147879872	E070	-29123
chr6	147879997	147880778	E070	-28217
chr6	147924633	147924823	E070	15638
chr6	147925107	147925157	E070	16112
chr6	147905560	147905612	E081	-3383
chr6	147906542	147906626	E081	-2369
chr6	147906709	147906804	E081	-2191
chr6	147906955	147907730	E081	-1265
chr6	147908923	147909155	E081	0
chr6	147909176	147909313	E081	181
chr6	147909700	147909794	E081	705
chr6	147910140	147910190	E081	1145
chr6	147910489	147911493	E081	1494
chr6	147922652	147922740	E081	13657
chr6	147922751	147922821	E081	13756
chr6	147922876	147923316	E081	13881
chr6	147906542	147906626	E082	-2369
chr6	147906709	147906804	E082	-2191
chr6	147906955	147907730	E082	-1265
chr6	147910489	147911493	E082	1494

rs844562