rs12467557

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

NRXN1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0087 (2597/29866,GnomAD)
G=0097 (2840/29116,TOPMED)
G=0200 (1000/5008,1000G)
G=0056 (214/3854,ALSPAC)
G=0054 (200/3708,TWINSUK)

Position: chr2:51015132 (GRCh38.p7) (2p16.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 65 Enhancers around

Promoter: 126 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.51015132A>G
GRCh37.p13 chr 2	NC_000002.11:g.51242270A>G
NRXN1 RefSeqGene	NG_011878.1:g.22405T>C

Gene: NRXN1, neurexin 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NRXN1 transcript variant alpha2	NM_001135659.1:c.	N/A	Intron Variant
NRXN1 transcript variant alpha1	NM_004801.4:c.	N/A	Intron Variant
NRXN1 transcript variant gamma1	NM_001320156.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant gamma2	NM_001320157.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant beta	NM_138735.2:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X10	XM_005264642.3:c.	N/A	Intron Variant
NRXN1 transcript variant X23	XM_005264643.3:c.	N/A	Intron Variant
NRXN1 transcript variant X31	XM_006712137.3:c.	N/A	Intron Variant
NRXN1 transcript variant X43	XM_006712140.3:c.	N/A	Intron Variant
NRXN1 transcript variant X7	XM_011533167.2:c.	N/A	Intron Variant
NRXN1 transcript variant X12	XM_011533171.2:c.	N/A	Intron Variant
NRXN1 transcript variant X14	XM_011533172.2:c.	N/A	Intron Variant
NRXN1 transcript variant X20	XM_011533174.2:c.	N/A	Intron Variant
NRXN1 transcript variant X24	XM_011533175.2:c.	N/A	Intron Variant
NRXN1 transcript variant X29	XM_011533177.2:c.	N/A	Intron Variant
NRXN1 transcript variant X30	XM_011533178.2:c.	N/A	Intron Variant
NRXN1 transcript variant X39	XM_011533180.2:c.	N/A	Intron Variant
NRXN1 transcript variant X1	XM_017005303.1:c.	N/A	Intron Variant
NRXN1 transcript variant X2	XM_017005304.1:c.	N/A	Intron Variant
NRXN1 transcript variant X3	XM_017005305.1:c.	N/A	Intron Variant
NRXN1 transcript variant X4	XM_017005306.1:c.	N/A	Intron Variant
NRXN1 transcript variant X5	XM_017005307.1:c.	N/A	Intron Variant
NRXN1 transcript variant X6	XM_017005308.1:c.	N/A	Intron Variant
NRXN1 transcript variant X8	XM_017005309.1:c.	N/A	Intron Variant
NRXN1 transcript variant X9	XM_017005310.1:c.	N/A	Intron Variant
NRXN1 transcript variant X11	XM_017005311.1:c.	N/A	Intron Variant
NRXN1 transcript variant X13	XM_017005312.1:c.	N/A	Intron Variant
NRXN1 transcript variant X15	XM_017005313.1:c.	N/A	Intron Variant
NRXN1 transcript variant X16	XM_017005314.1:c.	N/A	Intron Variant
NRXN1 transcript variant X17	XM_017005315.1:c.	N/A	Intron Variant
NRXN1 transcript variant X18	XM_017005316.1:c.	N/A	Intron Variant
NRXN1 transcript variant X19	XM_017005317.1:c.	N/A	Intron Variant
NRXN1 transcript variant X21	XM_017005318.1:c.	N/A	Intron Variant
NRXN1 transcript variant X22	XM_017005319.1:c.	N/A	Intron Variant
NRXN1 transcript variant X25	XM_017005320.1:c.	N/A	Intron Variant
NRXN1 transcript variant X26	XM_017005321.1:c.	N/A	Intron Variant
NRXN1 transcript variant X27	XM_017005322.1:c.	N/A	Intron Variant
NRXN1 transcript variant X28	XM_017005323.1:c.	N/A	Intron Variant
NRXN1 transcript variant X32	XM_017005324.1:c.	N/A	Intron Variant
NRXN1 transcript variant X33	XM_017005325.1:c.	N/A	Intron Variant
NRXN1 transcript variant X34	XM_017005326.1:c.	N/A	Intron Variant
NRXN1 transcript variant X35	XM_017005327.1:c.	N/A	Intron Variant
NRXN1 transcript variant X36	XM_017005328.1:c.	N/A	Intron Variant
NRXN1 transcript variant X37	XM_017005329.1:c.	N/A	Intron Variant
NRXN1 transcript variant X38	XM_017005330.1:c.	N/A	Intron Variant
NRXN1 transcript variant X40	XM_017005331.1:c.	N/A	Intron Variant
NRXN1 transcript variant X41	XM_017005332.1:c.	N/A	Intron Variant
NRXN1 transcript variant X42	XM_017005333.1:c.	N/A	Intron Variant
NRXN1 transcript variant X44	XM_011533183.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X45	XM_017005334.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X46	XM_017005335.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X47	XM_017005336.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X48	XM_017005337.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.902	G=0.098
1000Genomes	American	Sub	694	A=0.710	G=0.290
1000Genomes	East Asian	Sub	1008	A=0.548	G=0.452
1000Genomes	Europe	Sub	1006	A=0.962	G=0.038
1000Genomes	Global	Study-wide	5008	A=0.800	G=0.200
1000Genomes	South Asian	Sub	978	A=0.820	G=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.944	G=0.056
The Genome Aggregation Database	African	Sub	8706	A=0.912	G=0.088
The Genome Aggregation Database	American	Sub	832	A=0.690	G=0.310
The Genome Aggregation Database	East Asian	Sub	1554	A=0.565	G=0.435
The Genome Aggregation Database	Europe	Sub	18474	A=0.952	G=0.047
The Genome Aggregation Database	Global	Study-wide	29866	A=0.913	G=0.087
The Genome Aggregation Database	Other	Sub	300	A=0.960	G=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.902	G=0.097
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.946	G=0.054

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet
18270208	Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers.	Nussbaum J	Hum Mol Genet
24633560	Identification of candidate single-nucleotide polymorphisms in NRXN1 related to antipsychotic treatment response in patients with schizophrenia.	Jenkins A	Neuropsychopharmacology
20860064	Influence of neurexin 1 (NRXN1) polymorphisms in clozapine response.	Souza RP	Hum Psychopharmacol

P-Value

SNP ID	p-value	Traits	Study
rs12467557	6.88E-05	nicotine dependence	17158188

eQTL of rs12467557 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 rs12467557 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 )
chr2	51228070	51228356	E067	-13914
chr2	51240153	51241327	E067	-943
chr2	51241335	51241472	E067	-798
chr2	51227282	51227401	E068	-14869
chr2	51228070	51228356	E068	-13914
chr2	51228435	51228551	E068	-13719
chr2	51238679	51238729	E068	-3541
chr2	51242027	51242088	E068	-182
chr2	51242151	51242230	E068	-40
chr2	51227282	51227401	E069	-14869
chr2	51228070	51228356	E069	-13914
chr2	51228435	51228551	E069	-13719
chr2	51238679	51238729	E069	-3541
chr2	51240153	51241327	E069	-943
chr2	51241335	51241472	E069	-798
chr2	51242027	51242088	E069	-182
chr2	51242151	51242230	E069	-40
chr2	51206492	51206551	E070	-35719
chr2	51238679	51238729	E070	-3541
chr2	51240153	51241327	E070	-943
chr2	51241335	51241472	E070	-798
chr2	51242027	51242088	E070	-182
chr2	51242151	51242230	E070	-40
chr2	51246270	51246320	E070	4000
chr2	51227282	51227401	E071	-14869
chr2	51228070	51228356	E071	-13914
chr2	51228435	51228551	E071	-13719
chr2	51238679	51238729	E071	-3541
chr2	51241335	51241472	E071	-798
chr2	51242027	51242088	E071	-182
chr2	51242151	51242230	E071	-40
chr2	51228070	51228356	E072	-13914
chr2	51238679	51238729	E072	-3541
chr2	51240153	51241327	E073	-943
chr2	51241335	51241472	E073	-798
chr2	51242027	51242088	E073	-182
chr2	51242151	51242230	E073	-40
chr2	51245135	51245459	E073	2865
chr2	51227282	51227401	E074	-14869
chr2	51230851	51231029	E074	-11241
chr2	51231066	51231171	E074	-11099
chr2	51231191	51231256	E074	-11014
chr2	51240153	51241327	E074	-943
chr2	51241335	51241472	E074	-798
chr2	51206492	51206551	E081	-35719
chr2	51219684	51219740	E081	-22530
chr2	51219873	51219939	E081	-22331
chr2	51227282	51227401	E081	-14869
chr2	51238679	51238729	E081	-3541
chr2	51240153	51241327	E081	-943
chr2	51241335	51241472	E081	-798
chr2	51242027	51242088	E081	-182
chr2	51242151	51242230	E081	-40
chr2	51245031	51245086	E081	2761
chr2	51245135	51245459	E081	2865
chr2	51206492	51206551	E082	-35719
chr2	51219684	51219740	E082	-22530
chr2	51219873	51219939	E082	-22331
chr2	51227282	51227401	E082	-14869
chr2	51228070	51228356	E082	-13914
chr2	51242027	51242088	E082	-182
chr2	51242151	51242230	E082	-40
chr2	51245031	51245086	E082	2761
chr2	51245135	51245459	E082	2865
chr2	51260665	51260715	E082	18395

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	51252834	51252886	E067	10564
chr2	51252923	51252976	E067	10653
chr2	51253059	51253296	E067	10789
chr2	51253370	51253432	E067	11100
chr2	51253491	51253614	E067	11221
chr2	51253649	51253711	E067	11379
chr2	51253894	51253959	E067	11624
chr2	51253997	51254090	E067	11727
chr2	51255773	51255891	E067	13503
chr2	51256078	51256142	E067	13808
chr2	51256146	51256214	E067	13876
chr2	51257511	51257649	E067	15241
chr2	51258098	51258162	E067	15828
chr2	51258220	51258274	E067	15950
chr2	51258632	51260408	E067	16362
chr2	51252834	51252886	E068	10564
chr2	51252923	51252976	E068	10653
chr2	51253059	51253296	E068	10789
chr2	51253370	51253432	E068	11100
chr2	51253491	51253614	E068	11221
chr2	51253649	51253711	E068	11379
chr2	51253894	51253959	E068	11624
chr2	51253997	51254090	E068	11727
chr2	51257511	51257649	E068	15241
chr2	51258098	51258162	E068	15828
chr2	51258220	51258274	E068	15950
chr2	51258632	51260408	E068	16362
chr2	51253370	51253432	E069	11100
chr2	51253491	51253614	E069	11221
chr2	51253649	51253711	E069	11379
chr2	51253894	51253959	E069	11624
chr2	51253997	51254090	E069	11727
chr2	51255773	51255891	E069	13503
chr2	51256078	51256142	E069	13808
chr2	51256146	51256214	E069	13876
chr2	51257511	51257649	E069	15241
chr2	51258098	51258162	E069	15828
chr2	51258220	51258274	E069	15950
chr2	51258632	51260408	E069	16362
chr2	51252834	51252886	E070	10564
chr2	51252923	51252976	E070	10653
chr2	51253059	51253296	E070	10789
chr2	51253370	51253432	E070	11100
chr2	51253491	51253614	E070	11221
chr2	51253649	51253711	E070	11379
chr2	51253894	51253959	E070	11624
chr2	51253997	51254090	E070	11727
chr2	51257511	51257649	E070	15241
chr2	51258098	51258162	E070	15828
chr2	51258220	51258274	E070	15950
chr2	51258632	51260408	E070	16362
chr2	51253059	51253296	E071	10789
chr2	51253370	51253432	E071	11100
chr2	51253491	51253614	E071	11221
chr2	51253649	51253711	E071	11379
chr2	51253894	51253959	E071	11624
chr2	51253997	51254090	E071	11727
chr2	51255773	51255891	E071	13503
chr2	51256078	51256142	E071	13808
chr2	51256146	51256214	E071	13876
chr2	51257511	51257649	E071	15241
chr2	51258098	51258162	E071	15828
chr2	51258220	51258274	E071	15950
chr2	51258632	51260408	E071	16362
chr2	51252834	51252886	E072	10564
chr2	51252923	51252976	E072	10653
chr2	51253059	51253296	E072	10789
chr2	51253370	51253432	E072	11100
chr2	51253491	51253614	E072	11221
chr2	51253649	51253711	E072	11379
chr2	51253894	51253959	E072	11624
chr2	51253997	51254090	E072	11727
chr2	51255773	51255891	E072	13503
chr2	51256078	51256142	E072	13808
chr2	51256146	51256214	E072	13876
chr2	51257511	51257649	E072	15241
chr2	51258098	51258162	E072	15828
chr2	51258220	51258274	E072	15950
chr2	51258632	51260408	E072	16362
chr2	51252834	51252886	E073	10564
chr2	51252923	51252976	E073	10653
chr2	51253059	51253296	E073	10789
chr2	51253370	51253432	E073	11100
chr2	51253491	51253614	E073	11221
chr2	51253649	51253711	E073	11379
chr2	51253894	51253959	E073	11624
chr2	51253997	51254090	E073	11727
chr2	51255773	51255891	E073	13503
chr2	51256078	51256142	E073	13808
chr2	51256146	51256214	E073	13876
chr2	51257511	51257649	E073	15241
chr2	51258098	51258162	E073	15828
chr2	51258220	51258274	E073	15950
chr2	51258632	51260408	E073	16362
chr2	51253491	51253614	E074	11221
chr2	51253649	51253711	E074	11379
chr2	51253894	51253959	E074	11624
chr2	51253997	51254090	E074	11727
chr2	51257511	51257649	E074	15241
chr2	51258098	51258162	E074	15828
chr2	51258220	51258274	E074	15950
chr2	51258632	51260408	E074	16362
chr2	51252834	51252886	E081	10564
chr2	51252923	51252976	E081	10653
chr2	51253059	51253296	E081	10789
chr2	51253370	51253432	E081	11100
chr2	51253491	51253614	E081	11221
chr2	51253649	51253711	E081	11379
chr2	51253894	51253959	E081	11624
chr2	51253997	51254090	E081	11727
chr2	51257511	51257649	E081	15241
chr2	51258098	51258162	E081	15828
chr2	51258220	51258274	E081	15950
chr2	51258632	51260408	E081	16362
chr2	51252834	51252886	E082	10564
chr2	51252923	51252976	E082	10653
chr2	51253059	51253296	E082	10789
chr2	51253370	51253432	E082	11100
chr2	51253491	51253614	E082	11221
chr2	51253649	51253711	E082	11379
chr2	51253894	51253959	E082	11624
chr2	51253997	51254090	E082	11727
chr2	51257511	51257649	E082	15241
chr2	51258098	51258162	E082	15828
chr2	51258220	51258274	E082	15950
chr2	51258632	51260408	E082	16362