SNP Detail Info-rs11125007

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LINC01121 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0376 (11242/29890,GnomAD)
G==0415 (12093/29118,TOPMED)
G==0385 (1928/5008,1000G)
G==0335 (1292/3854,ALSPAC)
G==0320 (1186/3708,TWINSUK)

Position: chr2:45198965 (GRCh38.p7) (2p21)

Phenotype: CD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 34 Enhancers around

Promoter: 4 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.45198965G>A
GRCh37.p13 chr 2	NC_000002.11:g.45426104G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01121 transcript	NR_033831.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.521	A=0.479
1000Genomes	American	Sub	694	G=0.420	A=0.580
1000Genomes	East Asian	Sub	1008	G=0.368	A=0.632
1000Genomes	Europe	Sub	1006	G=0.358	A=0.642
1000Genomes	Global	Study-wide	5008	G=0.385	A=0.615
1000Genomes	South Asian	Sub	978	G=0.220	A=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.335	A=0.665
The Genome Aggregation Database	African	Sub	8694	G=0.484	A=0.516
The Genome Aggregation Database	American	Sub	838	G=0.400	A=0.600
The Genome Aggregation Database	East Asian	Sub	1618	G=0.342	A=0.658
The Genome Aggregation Database	Europe	Sub	18438	G=0.328	A=0.671
The Genome Aggregation Database	Global	Study-wide	29890	G=0.376	A=0.623
The Genome Aggregation Database	Other	Sub	302	G=0.310	A=0.690
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.415	A=0.584
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.320	A=0.680

PMID	Title	Author	Journal
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry

SNP ID	p-value	Traits	Study
rs11125007	0.0000904	cocaine dependence	23958962
rs11125007	0.00045	cocaine dependence,AA	23958962

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 )
chr2	45468619	45468765	E068	42515
chr2	45468897	45469041	E068	42793
chr2	45469127	45469255	E068	43023
chr2	45469341	45469981	E068	43237
chr2	45470104	45470223	E068	44000
chr2	45469127	45469255	E069	43023
chr2	45469341	45469981	E069	43237
chr2	45417910	45418027	E070	-8077
chr2	45418123	45418228	E070	-7876
chr2	45418294	45418571	E070	-7533
chr2	45418585	45418688	E070	-7416
chr2	45418813	45418935	E070	-7169
chr2	45418967	45419630	E070	-6474
chr2	45419872	45419997	E070	-6107
chr2	45468619	45468765	E070	42515
chr2	45469341	45469981	E070	43237
chr2	45395002	45395397	E071	-30707
chr2	45395401	45395570	E071	-30534
chr2	45468619	45468765	E071	42515
chr2	45468897	45469041	E071	42793
chr2	45469127	45469255	E071	43023
chr2	45469341	45469981	E071	43237
chr2	45470104	45470223	E071	44000
chr2	45468897	45469041	E074	42793
chr2	45469127	45469255	E074	43023
chr2	45469341	45469981	E074	43237
chr2	45417682	45417820	E081	-8284
chr2	45417910	45418027	E081	-8077
chr2	45418123	45418228	E081	-7876
chr2	45418294	45418571	E081	-7533
chr2	45418585	45418688	E081	-7416
chr2	45418813	45418935	E081	-7169
chr2	45418585	45418688	E082	-7416
chr2	45418813	45418935	E082	-7169

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	45395700	45398693	E068	-27411
chr2	45395700	45398693	E071	-27411
chr2	45395700	45398693	E074	-27411
chr2	45395700	45398693	E082	-27411

rs11125007