rs13382584

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NRXN1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0282 (8351/29550,GnomAD)
C=0256 (7462/29116,TOPMED)
C=0212 (1063/5008,1000G)
C=0333 (1284/3854,ALSPAC)
C=0335 (1243/3708,TWINSUK)

Position: chr2:51020156 (GRCh38.p7) (2p16.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 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.51020156T>C
GRCh37.p13 chr 2	NC_000002.11:g.51247294T>C
NRXN1 RefSeqGene	NG_011878.1:g.17381A>G

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	T=0.818	C=0.182
1000Genomes	American	Sub	694	T=0.800	C=0.200
1000Genomes	East Asian	Sub	1008	T=0.835	C=0.165
1000Genomes	Europe	Sub	1006	T=0.702	C=0.298
1000Genomes	Global	Study-wide	5008	T=0.788	C=0.212
1000Genomes	South Asian	Sub	978	T=0.780	C=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.667	C=0.333
The Genome Aggregation Database	African	Sub	8656	T=0.786	C=0.214
The Genome Aggregation Database	American	Sub	826	T=0.810	C=0.190
The Genome Aggregation Database	East Asian	Sub	1584	T=0.831	C=0.169
The Genome Aggregation Database	Europe	Sub	18182	T=0.670	C=0.329
The Genome Aggregation Database	Global	Study-wide	29550	T=0.717	C=0.282
The Genome Aggregation Database	Other	Sub	302	T=0.690	C=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.743	C=0.256
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.665	C=0.335

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
21477380	A case-control association study of NRXN1 polymorphisms with schizophrenia in Chinese Han population.	Yue W	Behav Brain Funct

P-Value

SNP ID	p-value	Traits	Study
rs13382584	0.000712	alcohol dependence	20201924

eQTL of rs13382584 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 rs13382584 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg10917619	chr2:51255627	NRXN1	-0.112581434101789	5.7023e-19

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	-18938
chr2	51240153	51241327	E067	-5967
chr2	51241335	51241472	E067	-5822
chr2	51227282	51227401	E068	-19893
chr2	51228070	51228356	E068	-18938
chr2	51228435	51228551	E068	-18743
chr2	51238679	51238729	E068	-8565
chr2	51242027	51242088	E068	-5206
chr2	51242151	51242230	E068	-5064
chr2	51227282	51227401	E069	-19893
chr2	51228070	51228356	E069	-18938
chr2	51228435	51228551	E069	-18743
chr2	51238679	51238729	E069	-8565
chr2	51240153	51241327	E069	-5967
chr2	51241335	51241472	E069	-5822
chr2	51242027	51242088	E069	-5206
chr2	51242151	51242230	E069	-5064
chr2	51206492	51206551	E070	-40743
chr2	51238679	51238729	E070	-8565
chr2	51240153	51241327	E070	-5967
chr2	51241335	51241472	E070	-5822
chr2	51242027	51242088	E070	-5206
chr2	51242151	51242230	E070	-5064
chr2	51246270	51246320	E070	-974
chr2	51227282	51227401	E071	-19893
chr2	51228070	51228356	E071	-18938
chr2	51228435	51228551	E071	-18743
chr2	51238679	51238729	E071	-8565
chr2	51241335	51241472	E071	-5822
chr2	51242027	51242088	E071	-5206
chr2	51242151	51242230	E071	-5064
chr2	51228070	51228356	E072	-18938
chr2	51238679	51238729	E072	-8565
chr2	51240153	51241327	E073	-5967
chr2	51241335	51241472	E073	-5822
chr2	51242027	51242088	E073	-5206
chr2	51242151	51242230	E073	-5064
chr2	51245135	51245459	E073	-1835
chr2	51227282	51227401	E074	-19893
chr2	51230851	51231029	E074	-16265
chr2	51231066	51231171	E074	-16123
chr2	51231191	51231256	E074	-16038
chr2	51240153	51241327	E074	-5967
chr2	51241335	51241472	E074	-5822
chr2	51206492	51206551	E081	-40743
chr2	51219684	51219740	E081	-27554
chr2	51219873	51219939	E081	-27355
chr2	51227282	51227401	E081	-19893
chr2	51238679	51238729	E081	-8565
chr2	51240153	51241327	E081	-5967
chr2	51241335	51241472	E081	-5822
chr2	51242027	51242088	E081	-5206
chr2	51242151	51242230	E081	-5064
chr2	51245031	51245086	E081	-2208
chr2	51245135	51245459	E081	-1835
chr2	51206492	51206551	E082	-40743
chr2	51219684	51219740	E082	-27554
chr2	51219873	51219939	E082	-27355
chr2	51227282	51227401	E082	-19893
chr2	51228070	51228356	E082	-18938
chr2	51242027	51242088	E082	-5206
chr2	51242151	51242230	E082	-5064
chr2	51245031	51245086	E082	-2208
chr2	51245135	51245459	E082	-1835
chr2	51260665	51260715	E082	13371

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	51252834	51252886	E067	5540
chr2	51252923	51252976	E067	5629
chr2	51253059	51253296	E067	5765
chr2	51253370	51253432	E067	6076
chr2	51253491	51253614	E067	6197
chr2	51253649	51253711	E067	6355
chr2	51253894	51253959	E067	6600
chr2	51253997	51254090	E067	6703
chr2	51255773	51255891	E067	8479
chr2	51256078	51256142	E067	8784
chr2	51256146	51256214	E067	8852
chr2	51257511	51257649	E067	10217
chr2	51258098	51258162	E067	10804
chr2	51258220	51258274	E067	10926
chr2	51258632	51260408	E067	11338
chr2	51252834	51252886	E068	5540
chr2	51252923	51252976	E068	5629
chr2	51253059	51253296	E068	5765
chr2	51253370	51253432	E068	6076
chr2	51253491	51253614	E068	6197
chr2	51253649	51253711	E068	6355
chr2	51253894	51253959	E068	6600
chr2	51253997	51254090	E068	6703
chr2	51257511	51257649	E068	10217
chr2	51258098	51258162	E068	10804
chr2	51258220	51258274	E068	10926
chr2	51258632	51260408	E068	11338
chr2	51253370	51253432	E069	6076
chr2	51253491	51253614	E069	6197
chr2	51253649	51253711	E069	6355
chr2	51253894	51253959	E069	6600
chr2	51253997	51254090	E069	6703
chr2	51255773	51255891	E069	8479
chr2	51256078	51256142	E069	8784
chr2	51256146	51256214	E069	8852
chr2	51257511	51257649	E069	10217
chr2	51258098	51258162	E069	10804
chr2	51258220	51258274	E069	10926
chr2	51258632	51260408	E069	11338
chr2	51252834	51252886	E070	5540
chr2	51252923	51252976	E070	5629
chr2	51253059	51253296	E070	5765
chr2	51253370	51253432	E070	6076
chr2	51253491	51253614	E070	6197
chr2	51253649	51253711	E070	6355
chr2	51253894	51253959	E070	6600
chr2	51253997	51254090	E070	6703
chr2	51257511	51257649	E070	10217
chr2	51258098	51258162	E070	10804
chr2	51258220	51258274	E070	10926
chr2	51258632	51260408	E070	11338
chr2	51253059	51253296	E071	5765
chr2	51253370	51253432	E071	6076
chr2	51253491	51253614	E071	6197
chr2	51253649	51253711	E071	6355
chr2	51253894	51253959	E071	6600
chr2	51253997	51254090	E071	6703
chr2	51255773	51255891	E071	8479
chr2	51256078	51256142	E071	8784
chr2	51256146	51256214	E071	8852
chr2	51257511	51257649	E071	10217
chr2	51258098	51258162	E071	10804
chr2	51258220	51258274	E071	10926
chr2	51258632	51260408	E071	11338
chr2	51252834	51252886	E072	5540
chr2	51252923	51252976	E072	5629
chr2	51253059	51253296	E072	5765
chr2	51253370	51253432	E072	6076
chr2	51253491	51253614	E072	6197
chr2	51253649	51253711	E072	6355
chr2	51253894	51253959	E072	6600
chr2	51253997	51254090	E072	6703
chr2	51255773	51255891	E072	8479
chr2	51256078	51256142	E072	8784
chr2	51256146	51256214	E072	8852
chr2	51257511	51257649	E072	10217
chr2	51258098	51258162	E072	10804
chr2	51258220	51258274	E072	10926
chr2	51258632	51260408	E072	11338
chr2	51252834	51252886	E073	5540
chr2	51252923	51252976	E073	5629
chr2	51253059	51253296	E073	5765
chr2	51253370	51253432	E073	6076
chr2	51253491	51253614	E073	6197
chr2	51253649	51253711	E073	6355
chr2	51253894	51253959	E073	6600
chr2	51253997	51254090	E073	6703
chr2	51255773	51255891	E073	8479
chr2	51256078	51256142	E073	8784
chr2	51256146	51256214	E073	8852
chr2	51257511	51257649	E073	10217
chr2	51258098	51258162	E073	10804
chr2	51258220	51258274	E073	10926
chr2	51258632	51260408	E073	11338
chr2	51253491	51253614	E074	6197
chr2	51253649	51253711	E074	6355
chr2	51253894	51253959	E074	6600
chr2	51253997	51254090	E074	6703
chr2	51257511	51257649	E074	10217
chr2	51258098	51258162	E074	10804
chr2	51258220	51258274	E074	10926
chr2	51258632	51260408	E074	11338
chr2	51252834	51252886	E081	5540
chr2	51252923	51252976	E081	5629
chr2	51253059	51253296	E081	5765
chr2	51253370	51253432	E081	6076
chr2	51253491	51253614	E081	6197
chr2	51253649	51253711	E081	6355
chr2	51253894	51253959	E081	6600
chr2	51253997	51254090	E081	6703
chr2	51257511	51257649	E081	10217
chr2	51258098	51258162	E081	10804
chr2	51258220	51258274	E081	10926
chr2	51258632	51260408	E081	11338
chr2	51252834	51252886	E082	5540
chr2	51252923	51252976	E082	5629
chr2	51253059	51253296	E082	5765
chr2	51253370	51253432	E082	6076
chr2	51253491	51253614	E082	6197
chr2	51253649	51253711	E082	6355
chr2	51253894	51253959	E082	6600
chr2	51253997	51254090	E082	6703
chr2	51257511	51257649	E082	10217
chr2	51258098	51258162	E082	10804
chr2	51258220	51258274	E082	10926
chr2	51258632	51260408	E082	11338