rs12623467

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

NRXN1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0105 (2881/27394,GnomAD)
T=0227 (1136/5008,1000G)
T=0056 (215/3854,ALSPAC)
T=0054 (199/3708,TWINSUK)

Position: chr2:50997951 (GRCh38.p7) (2p16.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 5 publication(s)

Genomic View: See rs on genome

Enhancer: 78 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.50997951C>T
GRCh37.p13 chr 2	NC_000002.11:g.51225089C>T
NRXN1 RefSeqGene	NG_011878.1:g.39586G>A

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	C=0.868	T=0.132
1000Genomes	American	Sub	694	C=0.700	T=0.300
1000Genomes	East Asian	Sub	1008	C=0.483	T=0.517
1000Genomes	Europe	Sub	1006	C=0.963	T=0.037
1000Genomes	Global	Study-wide	5008	C=0.773	T=0.227
1000Genomes	South Asian	Sub	978	C=0.800	T=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.944	T=0.056
The Genome Aggregation Database	African	Sub	6756	C=0.864	T=0.136
The Genome Aggregation Database	American	Sub	828	C=0.670	T=0.330
The Genome Aggregation Database	East Asian	Sub	1458	C=0.501	T=0.499
The Genome Aggregation Database	Europe	Sub	18060	C=0.947	T=0.052
The Genome Aggregation Database	Global	Study-wide	27394	C=0.894	T=0.105
The Genome Aggregation Database	Other	Sub	292	C=0.960	T=0.040
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.946	T=0.054

PMID	Title	Author	Journal
21687627	Neurexin-1 and frontal lobe white matter: an overlapping intermediate phenotype for schizophrenia and autism spectrum disorders.	Voineskos AN	PLoS One
18565990	Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.	Saccone SF	Bioinformatics
18783506	Association of a single nucleotide polymorphism in neuronal acetylcholine receptor subunit alpha 5 (CHRNA5) with smoking status and with 'pleasurable buzz' during early experimentation with smoking.	Sherva R	Addiction
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

P-Value

SNP ID	p-value	Traits	Study
rs12623467	1.48E-05	nicotine dependence	17158188

eQTL of rs12623467 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 rs12623467 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	2981
chr2	51240153	51241327	E067	15064
chr2	51241335	51241472	E067	16246
chr2	51184508	51184668	E068	-40421
chr2	51185169	51185324	E068	-39765
chr2	51227282	51227401	E068	2193
chr2	51228070	51228356	E068	2981
chr2	51228435	51228551	E068	3346
chr2	51238679	51238729	E068	13590
chr2	51242027	51242088	E068	16938
chr2	51242151	51242230	E068	17062
chr2	51185169	51185324	E069	-39765
chr2	51227282	51227401	E069	2193
chr2	51228070	51228356	E069	2981
chr2	51228435	51228551	E069	3346
chr2	51238679	51238729	E069	13590
chr2	51240153	51241327	E069	15064
chr2	51241335	51241472	E069	16246
chr2	51242027	51242088	E069	16938
chr2	51242151	51242230	E069	17062
chr2	51175794	51176069	E070	-49020
chr2	51182272	51182488	E070	-42601
chr2	51184508	51184668	E070	-40421
chr2	51185169	51185324	E070	-39765
chr2	51206492	51206551	E070	-18538
chr2	51238679	51238729	E070	13590
chr2	51240153	51241327	E070	15064
chr2	51241335	51241472	E070	16246
chr2	51242027	51242088	E070	16938
chr2	51242151	51242230	E070	17062
chr2	51246270	51246320	E070	21181
chr2	51184103	51184432	E071	-40657
chr2	51184508	51184668	E071	-40421
chr2	51185169	51185324	E071	-39765
chr2	51227282	51227401	E071	2193
chr2	51228070	51228356	E071	2981
chr2	51228435	51228551	E071	3346
chr2	51238679	51238729	E071	13590
chr2	51241335	51241472	E071	16246
chr2	51242027	51242088	E071	16938
chr2	51242151	51242230	E071	17062
chr2	51228070	51228356	E072	2981
chr2	51238679	51238729	E072	13590
chr2	51182272	51182488	E073	-42601
chr2	51240153	51241327	E073	15064
chr2	51241335	51241472	E073	16246
chr2	51242027	51242088	E073	16938
chr2	51242151	51242230	E073	17062
chr2	51245135	51245459	E073	20046
chr2	51176676	51177278	E074	-47811
chr2	51182272	51182488	E074	-42601
chr2	51227282	51227401	E074	2193
chr2	51230851	51231029	E074	5762
chr2	51231066	51231171	E074	5977
chr2	51231191	51231256	E074	6102
chr2	51240153	51241327	E074	15064
chr2	51241335	51241472	E074	16246
chr2	51206492	51206551	E081	-18538
chr2	51219684	51219740	E081	-5349
chr2	51219873	51219939	E081	-5150
chr2	51227282	51227401	E081	2193
chr2	51238679	51238729	E081	13590
chr2	51240153	51241327	E081	15064
chr2	51241335	51241472	E081	16246
chr2	51242027	51242088	E081	16938
chr2	51242151	51242230	E081	17062
chr2	51245031	51245086	E081	19942
chr2	51245135	51245459	E081	20046
chr2	51206492	51206551	E082	-18538
chr2	51219684	51219740	E082	-5349
chr2	51219873	51219939	E082	-5150
chr2	51227282	51227401	E082	2193
chr2	51228070	51228356	E082	2981
chr2	51242027	51242088	E082	16938
chr2	51242151	51242230	E082	17062
chr2	51245031	51245086	E082	19942
chr2	51245135	51245459	E082	20046
chr2	51260665	51260715	E082	35576

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	51252834	51252886	E067	27745
chr2	51252923	51252976	E067	27834
chr2	51253059	51253296	E067	27970
chr2	51253370	51253432	E067	28281
chr2	51253491	51253614	E067	28402
chr2	51253649	51253711	E067	28560
chr2	51253894	51253959	E067	28805
chr2	51253997	51254090	E067	28908
chr2	51255773	51255891	E067	30684
chr2	51256078	51256142	E067	30989
chr2	51256146	51256214	E067	31057
chr2	51257511	51257649	E067	32422
chr2	51258098	51258162	E067	33009
chr2	51258220	51258274	E067	33131
chr2	51258632	51260408	E067	33543
chr2	51252834	51252886	E068	27745
chr2	51252923	51252976	E068	27834
chr2	51253059	51253296	E068	27970
chr2	51253370	51253432	E068	28281
chr2	51253491	51253614	E068	28402
chr2	51253649	51253711	E068	28560
chr2	51253894	51253959	E068	28805
chr2	51253997	51254090	E068	28908
chr2	51257511	51257649	E068	32422
chr2	51258098	51258162	E068	33009
chr2	51258220	51258274	E068	33131
chr2	51258632	51260408	E068	33543
chr2	51253370	51253432	E069	28281
chr2	51253491	51253614	E069	28402
chr2	51253649	51253711	E069	28560
chr2	51253894	51253959	E069	28805
chr2	51253997	51254090	E069	28908
chr2	51255773	51255891	E069	30684
chr2	51256078	51256142	E069	30989
chr2	51256146	51256214	E069	31057
chr2	51257511	51257649	E069	32422
chr2	51258098	51258162	E069	33009
chr2	51258220	51258274	E069	33131
chr2	51258632	51260408	E069	33543
chr2	51252834	51252886	E070	27745
chr2	51252923	51252976	E070	27834
chr2	51253059	51253296	E070	27970
chr2	51253370	51253432	E070	28281
chr2	51253491	51253614	E070	28402
chr2	51253649	51253711	E070	28560
chr2	51253894	51253959	E070	28805
chr2	51253997	51254090	E070	28908
chr2	51257511	51257649	E070	32422
chr2	51258098	51258162	E070	33009
chr2	51258220	51258274	E070	33131
chr2	51258632	51260408	E070	33543
chr2	51253059	51253296	E071	27970
chr2	51253370	51253432	E071	28281
chr2	51253491	51253614	E071	28402
chr2	51253649	51253711	E071	28560
chr2	51253894	51253959	E071	28805
chr2	51253997	51254090	E071	28908
chr2	51255773	51255891	E071	30684
chr2	51256078	51256142	E071	30989
chr2	51256146	51256214	E071	31057
chr2	51257511	51257649	E071	32422
chr2	51258098	51258162	E071	33009
chr2	51258220	51258274	E071	33131
chr2	51258632	51260408	E071	33543
chr2	51252834	51252886	E072	27745
chr2	51252923	51252976	E072	27834
chr2	51253059	51253296	E072	27970
chr2	51253370	51253432	E072	28281
chr2	51253491	51253614	E072	28402
chr2	51253649	51253711	E072	28560
chr2	51253894	51253959	E072	28805
chr2	51253997	51254090	E072	28908
chr2	51255773	51255891	E072	30684
chr2	51256078	51256142	E072	30989
chr2	51256146	51256214	E072	31057
chr2	51257511	51257649	E072	32422
chr2	51258098	51258162	E072	33009
chr2	51258220	51258274	E072	33131
chr2	51258632	51260408	E072	33543
chr2	51252834	51252886	E073	27745
chr2	51252923	51252976	E073	27834
chr2	51253059	51253296	E073	27970
chr2	51253370	51253432	E073	28281
chr2	51253491	51253614	E073	28402
chr2	51253649	51253711	E073	28560
chr2	51253894	51253959	E073	28805
chr2	51253997	51254090	E073	28908
chr2	51255773	51255891	E073	30684
chr2	51256078	51256142	E073	30989
chr2	51256146	51256214	E073	31057
chr2	51257511	51257649	E073	32422
chr2	51258098	51258162	E073	33009
chr2	51258220	51258274	E073	33131
chr2	51258632	51260408	E073	33543
chr2	51253491	51253614	E074	28402
chr2	51253649	51253711	E074	28560
chr2	51253894	51253959	E074	28805
chr2	51253997	51254090	E074	28908
chr2	51257511	51257649	E074	32422
chr2	51258098	51258162	E074	33009
chr2	51258220	51258274	E074	33131
chr2	51258632	51260408	E074	33543
chr2	51252834	51252886	E081	27745
chr2	51252923	51252976	E081	27834
chr2	51253059	51253296	E081	27970
chr2	51253370	51253432	E081	28281
chr2	51253491	51253614	E081	28402
chr2	51253649	51253711	E081	28560
chr2	51253894	51253959	E081	28805
chr2	51253997	51254090	E081	28908
chr2	51257511	51257649	E081	32422
chr2	51258098	51258162	E081	33009
chr2	51258220	51258274	E081	33131
chr2	51258632	51260408	E081	33543
chr2	51252834	51252886	E082	27745
chr2	51252923	51252976	E082	27834
chr2	51253059	51253296	E082	27970
chr2	51253370	51253432	E082	28281
chr2	51253491	51253614	E082	28402
chr2	51253649	51253711	E082	28560
chr2	51253894	51253959	E082	28805
chr2	51253997	51254090	E082	28908
chr2	51257511	51257649	E082	32422
chr2	51258098	51258162	E082	33009
chr2	51258220	51258274	E082	33131
chr2	51258632	51260408	E082	33543