rs2293843

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

NRXN3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0442 (13229/29876,GnomAD)
T=0444 (12950/29118,TOPMED)
T=0475 (2380/5008,1000G)
T=0384 (1479/3854,ALSPAC)
T=0385 (1426/3708,TWINSUK)

Position: chr14:79854405 (GRCh38.p7) (14q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 125 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 14	NC_000014.9:g.79854405C>T
GRCh37.p13 chr 14	NC_000014.8:g.80320748C>T

Gene: NRXN3, neurexin 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NRXN3 transcript variant 3	NM_001105250.2:c.	N/A	Intron Variant
NRXN3 transcript variant 4	NM_001272020.1:c.	N/A	Intron Variant
NRXN3 transcript variant 1	NM_004796.5:c.	N/A	Intron Variant
NRXN3 transcript variant 2	NM_138970.4:c.	N/A	Intron Variant
NRXN3 transcript variant 5	NR_073546.1:n.	N/A	Intron Variant
NRXN3 transcript variant 6	NR_073547.1:n.	N/A	Intron Variant
NRXN3 transcript variant X6	XM_005268218.2:c.	N/A	Intron Variant
NRXN3 transcript variant X7	XM_006720322.2:c.	N/A	Intron Variant
NRXN3 transcript variant X21	XM_006720323.2:c.	N/A	Intron Variant
NRXN3 transcript variant X1	XM_011537363.1:c.	N/A	Intron Variant
NRXN3 transcript variant X2	XM_011537364.2:c.	N/A	Intron Variant
NRXN3 transcript variant X5	XM_011537365.2:c.	N/A	Intron Variant
NRXN3 transcript variant X9	XM_011537366.1:c.	N/A	Intron Variant
NRXN3 transcript variant X15	XM_011537367.1:c.	N/A	Intron Variant
NRXN3 transcript variant X19	XM_011537368.1:c.	N/A	Intron Variant
NRXN3 transcript variant X20	XM_011537369.1:c.	N/A	Intron Variant
NRXN3 transcript variant X21	XM_011537370.1:c.	N/A	Intron Variant
NRXN3 transcript variant X25	XM_011537371.1:c.	N/A	Intron Variant
NRXN3 transcript variant X26	XM_011537372.1:c.	N/A	Intron Variant
NRXN3 transcript variant X31	XM_011537373.1:c.	N/A	Intron Variant
NRXN3 transcript variant X44	XM_011537377.2:c.	N/A	Intron Variant
NRXN3 transcript variant X3	XM_017021790.1:c.	N/A	Intron Variant
NRXN3 transcript variant X4	XM_017021791.1:c.	N/A	Intron Variant
NRXN3 transcript variant X8	XM_017021792.1:c.	N/A	Intron Variant
NRXN3 transcript variant X10	XM_017021793.1:c.	N/A	Intron Variant
NRXN3 transcript variant X11	XM_017021794.1:c.	N/A	Intron Variant
NRXN3 transcript variant X12	XM_017021795.1:c.	N/A	Intron Variant
NRXN3 transcript variant X13	XM_017021796.1:c.	N/A	Intron Variant
NRXN3 transcript variant X13	XM_017021797.1:c.	N/A	Intron Variant
NRXN3 transcript variant X14	XM_017021798.1:c.	N/A	Intron Variant
NRXN3 transcript variant X17	XM_017021799.1:c.	N/A	Intron Variant
NRXN3 transcript variant X22	XM_017021800.1:c.	N/A	Intron Variant
NRXN3 transcript variant X23	XM_017021801.1:c.	N/A	Intron Variant
NRXN3 transcript variant X24	XM_017021802.1:c.	N/A	Intron Variant
NRXN3 transcript variant X27	XM_017021803.1:c.	N/A	Intron Variant
NRXN3 transcript variant X28	XM_017021804.1:c.	N/A	Intron Variant
NRXN3 transcript variant X29	XM_017021805.1:c.	N/A	Intron Variant
NRXN3 transcript variant X30	XM_017021806.1:c.	N/A	Intron Variant
NRXN3 transcript variant X30	XM_017021807.1:c.	N/A	Intron Variant
NRXN3 transcript variant X32	XR_001750599.1:n.	N/A	Intron Variant
NRXN3 transcript variant X33	XR_001750600.1:n.	N/A	Intron Variant
NRXN3 transcript variant X34	XR_001750601.1:n.	N/A	Intron Variant
NRXN3 transcript variant X35	XR_001750602.1:n.	N/A	Intron Variant
NRXN3 transcript variant X36	XR_001750603.1:n.	N/A	Intron Variant
NRXN3 transcript variant X37	XR_001750604.1:n.	N/A	Intron Variant
NRXN3 transcript variant X38	XR_001750605.1:n.	N/A	Intron Variant
NRXN3 transcript variant X39	XR_001750606.1:n.	N/A	Intron Variant
NRXN3 transcript variant X40	XR_001750607.1:n.	N/A	Intron Variant
NRXN3 transcript variant X41	XR_001750608.1:n.	N/A	Intron Variant
NRXN3 transcript variant X44	XR_001750610.1:n.	N/A	Intron Variant
NRXN3 transcript variant X45	XR_943561.1:n.	N/A	Intron Variant
NRXN3 transcript variant X46	XR_943563.2:n.	N/A	Intron Variant
NRXN3 transcript variant X42	XR_001750609.1:n.	N/A	Genic Downstream Transcript Variant
NRXN3 transcript variant X47	XR_943562.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.436	T=0.564
1000Genomes	American	Sub	694	C=0.690	T=0.310
1000Genomes	East Asian	Sub	1008	C=0.444	T=0.556
1000Genomes	Europe	Sub	1006	C=0.657	T=0.343
1000Genomes	Global	Study-wide	5008	C=0.525	T=0.475
1000Genomes	South Asian	Sub	978	C=0.470	T=0.530
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.616	T=0.384
The Genome Aggregation Database	African	Sub	8708	C=0.459	T=0.541
The Genome Aggregation Database	American	Sub	836	C=0.680	T=0.320
The Genome Aggregation Database	East Asian	Sub	1606	C=0.414	T=0.586
The Genome Aggregation Database	Europe	Sub	18424	C=0.609	T=0.390
The Genome Aggregation Database	Global	Study-wide	29876	C=0.557	T=0.442
The Genome Aggregation Database	Other	Sub	302	C=0.670	T=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.555	T=0.444
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.615	T=0.385

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs2293843	0.000362	alcohol consumption (maxi-drinks)	24277619

eQTL of rs2293843 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 rs2293843 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 )
chr14	80287360	80287546	E067	-33202
chr14	80287593	80287773	E067	-32975
chr14	80287903	80288009	E067	-32739
chr14	80288399	80288449	E067	-32299
chr14	80288483	80288720	E067	-32028
chr14	80290402	80290459	E067	-30289
chr14	80291906	80291956	E067	-28792
chr14	80302170	80302273	E067	-18475
chr14	80324560	80324781	E067	3812
chr14	80324887	80324982	E067	4139
chr14	80325032	80325072	E067	4284
chr14	80287360	80287546	E068	-33202
chr14	80287593	80287773	E068	-32975
chr14	80287903	80288009	E068	-32739
chr14	80288483	80288720	E068	-32028
chr14	80290402	80290459	E068	-30289
chr14	80292844	80292944	E068	-27804
chr14	80293438	80293487	E068	-27261
chr14	80295829	80295891	E068	-24857
chr14	80296255	80296381	E068	-24367
chr14	80298690	80298780	E068	-21968
chr14	80324560	80324781	E068	3812
chr14	80324887	80324982	E068	4139
chr14	80276663	80276802	E069	-43946
chr14	80287360	80287546	E069	-33202
chr14	80287593	80287773	E069	-32975
chr14	80287903	80288009	E069	-32739
chr14	80288399	80288449	E069	-32299
chr14	80288483	80288720	E069	-32028
chr14	80289906	80289957	E069	-30791
chr14	80290402	80290459	E069	-30289
chr14	80291328	80291903	E069	-28845
chr14	80292844	80292944	E069	-27804
chr14	80296255	80296381	E069	-24367
chr14	80297231	80297282	E069	-23466
chr14	80297570	80297919	E069	-22829
chr14	80297936	80298165	E069	-22583
chr14	80298690	80298780	E069	-21968
chr14	80302711	80302779	E069	-17969
chr14	80324560	80324781	E069	3812
chr14	80324887	80324982	E069	4139
chr14	80325032	80325072	E069	4284
chr14	80287360	80287546	E070	-33202
chr14	80287593	80287773	E070	-32975
chr14	80295829	80295891	E070	-24857
chr14	80296255	80296381	E070	-24367
chr14	80297570	80297919	E070	-22829
chr14	80297936	80298165	E070	-22583
chr14	80324560	80324781	E070	3812
chr14	80324887	80324982	E070	4139
chr14	80344572	80345079	E070	23824
chr14	80345138	80345570	E070	24390
chr14	80345613	80345667	E070	24865
chr14	80276663	80276802	E071	-43946
chr14	80287360	80287546	E071	-33202
chr14	80287593	80287773	E071	-32975
chr14	80289906	80289957	E071	-30791
chr14	80290402	80290459	E071	-30289
chr14	80292844	80292944	E071	-27804
chr14	80293438	80293487	E071	-27261
chr14	80296999	80297049	E071	-23699
chr14	80297134	80297191	E071	-23557
chr14	80297231	80297282	E071	-23466
chr14	80297570	80297919	E071	-22829
chr14	80297936	80298165	E071	-22583
chr14	80300167	80300536	E071	-20212
chr14	80302170	80302273	E071	-18475
chr14	80302711	80302779	E071	-17969
chr14	80302832	80302923	E071	-17825
chr14	80303060	80303264	E071	-17484
chr14	80308021	80308247	E071	-12501
chr14	80308290	80308352	E071	-12396
chr14	80324560	80324781	E071	3812
chr14	80324887	80324982	E071	4139
chr14	80325032	80325072	E071	4284
chr14	80276663	80276802	E072	-43946
chr14	80280292	80280418	E072	-40330
chr14	80280625	80280675	E072	-40073
chr14	80286750	80286800	E072	-33948
chr14	80287360	80287546	E072	-33202
chr14	80287593	80287773	E072	-32975
chr14	80290402	80290459	E072	-30289
chr14	80292844	80292944	E072	-27804
chr14	80295829	80295891	E072	-24857
chr14	80296255	80296381	E072	-24367
chr14	80297570	80297919	E072	-22829
chr14	80297936	80298165	E072	-22583
chr14	80298690	80298780	E072	-21968
chr14	80302170	80302273	E072	-18475
chr14	80302711	80302779	E072	-17969
chr14	80302832	80302923	E072	-17825
chr14	80303060	80303264	E072	-17484
chr14	80308021	80308247	E072	-12501
chr14	80308290	80308352	E072	-12396
chr14	80308500	80308540	E072	-12208
chr14	80308700	80308920	E072	-11828
chr14	80324560	80324781	E072	3812
chr14	80324887	80324982	E072	4139
chr14	80287360	80287546	E073	-33202
chr14	80287593	80287773	E073	-32975
chr14	80286750	80286800	E074	-33948
chr14	80287360	80287546	E074	-33202
chr14	80287593	80287773	E074	-32975
chr14	80287903	80288009	E074	-32739
chr14	80288399	80288449	E074	-32299
chr14	80288483	80288720	E074	-32028
chr14	80289906	80289957	E074	-30791
chr14	80290402	80290459	E074	-30289
chr14	80292844	80292944	E074	-27804
chr14	80293438	80293487	E074	-27261
chr14	80295676	80295716	E074	-25032
chr14	80295829	80295891	E074	-24857
chr14	80296255	80296381	E074	-24367
chr14	80297570	80297919	E074	-22829
chr14	80297936	80298165	E074	-22583
chr14	80302170	80302273	E074	-18475
chr14	80307551	80307605	E074	-13143
chr14	80308021	80308247	E074	-12501
chr14	80308290	80308352	E074	-12396
chr14	80308500	80308540	E074	-12208
chr14	80308700	80308920	E074	-11828
chr14	80324560	80324781	E074	3812
chr14	80324887	80324982	E074	4139
chr14	80345138	80345570	E081	24390
chr14	80345613	80345667	E081	24865