rs1296438

Organism: Homo sapiens

Alleles: A>C / A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0398 (11904/29894,GnomAD)
G=0451 (13132/29118,TOPMED)
G=0469 (2347/5008,1000G)
G=0260 (1002/3854,ALSPAC)
G=0267 (991/3708,TWINSUK)

Position: chr1:53471504 (GRCh38.p7) (1p32.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 90 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.53471504A>C
GRCh38.p7 chr 1	NC_000001.11:g.53471504A>G
GRCh37.p13 chr 1	NC_000001.10:g.53937177A>C
GRCh37.p13 chr 1	NC_000001.10:g.53937177A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.258	G=0.742
1000Genomes	American	Sub	694	A=0.780	G=0.220
1000Genomes	East Asian	Sub	1008	A=0.468	G=0.532
1000Genomes	Europe	Sub	1006	A=0.724	G=0.276
1000Genomes	Global	Study-wide	5008	A=0.531	G=0.469
1000Genomes	South Asian	Sub	978	A=0.590	G=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.740	G=0.260
The Genome Aggregation Database	African	Sub	8706	A=0.306	C=0.000
The Genome Aggregation Database	American	Sub	836	A=0.820	C=0.00,
The Genome Aggregation Database	East Asian	Sub	1616	A=0.502	C=0.000
The Genome Aggregation Database	Europe	Sub	18436	A=0.738	C=0.000
The Genome Aggregation Database	Global	Study-wide	29894	A=0.601	C=0.000
The Genome Aggregation Database	Other	Sub	300	A=0.660	C=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.549	G=0.451
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.733	G=0.267

PMID	Title	Author	Journal
23942779	A genome-wide association study of behavioral disinhibition.	McGue M	Behav Genet

P-Value

SNP ID	p-value	Traits	Study
rs1296438	7.9E-06	nicotine use	23942779

eQTL of rs1296438 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 rs1296438 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 )
chr1	53882656	53883206	E067	-29874
chr1	53936226	53936439	E067	23146
chr1	53936459	53936605	E067	23379
chr1	53882656	53883206	E068	-29874
chr1	53936226	53936439	E068	23146
chr1	53936459	53936605	E068	23379
chr1	53882656	53883206	E069	-29874
chr1	53883523	53883596	E069	-29484
chr1	53883756	53883816	E069	-29264
chr1	53875267	53875401	E070	-37679
chr1	53875591	53875727	E070	-37353
chr1	53875853	53875999	E070	-37081
chr1	53876138	53876270	E070	-36810
chr1	53876464	53876604	E070	-36476
chr1	53878739	53879534	E070	-33546
chr1	53879879	53879967	E070	-33113
chr1	53880093	53880218	E070	-32862
chr1	53881062	53881221	E070	-31859
chr1	53881456	53881552	E070	-31528
chr1	53881647	53882517	E070	-30563
chr1	53883756	53883816	E070	-29264
chr1	53884803	53884961	E070	-28119
chr1	53886533	53886625	E070	-26455
chr1	53886783	53886851	E070	-26229
chr1	53896301	53896863	E070	-16217
chr1	53897223	53897344	E070	-15736
chr1	53928498	53928758	E070	15418
chr1	53935793	53936205	E070	22713
chr1	53940547	53940640	E070	27467
chr1	53940657	53940733	E070	27577
chr1	53882656	53883206	E071	-29874
chr1	53883523	53883596	E071	-29484
chr1	53935793	53936205	E071	22713
chr1	53936226	53936439	E071	23146
chr1	53936459	53936605	E071	23379
chr1	53951628	53951782	E071	38548
chr1	53879879	53879967	E072	-33113
chr1	53882656	53883206	E072	-29874
chr1	53936226	53936439	E072	23146
chr1	53936459	53936605	E072	23379
chr1	53943351	53943448	E072	30271
chr1	53943693	53943762	E072	30613
chr1	53951162	53951586	E072	38082
chr1	53935793	53936205	E073	22713
chr1	53936226	53936439	E073	23146
chr1	53936459	53936605	E073	23379
chr1	53882656	53883206	E074	-29874
chr1	53936459	53936605	E074	23379
chr1	53874790	53874844	E081	-38236
chr1	53875267	53875401	E081	-37679
chr1	53875591	53875727	E081	-37353
chr1	53875853	53875999	E081	-37081
chr1	53876138	53876270	E081	-36810
chr1	53878739	53879534	E081	-33546
chr1	53879879	53879967	E081	-33113
chr1	53880093	53880218	E081	-32862
chr1	53881062	53881221	E081	-31859
chr1	53881456	53881552	E081	-31528
chr1	53881647	53882517	E081	-30563
chr1	53882656	53883206	E081	-29874
chr1	53883523	53883596	E081	-29484
chr1	53883756	53883816	E081	-29264
chr1	53884803	53884961	E081	-28119
chr1	53895963	53896272	E081	-16808
chr1	53896301	53896863	E081	-16217
chr1	53920705	53920807	E081	7625
chr1	53928498	53928758	E081	15418
chr1	53929881	53930081	E081	16801
chr1	53930835	53931032	E081	17755
chr1	53951162	53951586	E081	38082
chr1	53951628	53951782	E081	38548
chr1	53874790	53874844	E082	-38236
chr1	53876464	53876604	E082	-36476
chr1	53878739	53879534	E082	-33546
chr1	53879879	53879967	E082	-33113
chr1	53880093	53880218	E082	-32862
chr1	53881062	53881221	E082	-31859
chr1	53881456	53881552	E082	-31528
chr1	53881647	53882517	E082	-30563
chr1	53883523	53883596	E082	-29484
chr1	53883756	53883816	E082	-29264
chr1	53884803	53884961	E082	-28119
chr1	53895963	53896272	E082	-16808
chr1	53896301	53896863	E082	-16217
chr1	53897223	53897344	E082	-15736
chr1	53920705	53920807	E082	7625
chr1	53928498	53928758	E082	15418
chr1	53929881	53930081	E082	16801
chr1	53944138	53944497	E082	31058
chr1	53945916	53945966	E082	32836