rs10799590

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CNIH3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0434 (12980/29846,GnomAD)
G==0409 (11921/29116,TOPMED)
G==0361 (1810/5008,1000G)
A=0448 (1727/3854,ALSPAC)
A=0454 (1685/3708,TWINSUK)

Position: chr1:224634780 (GRCh38.p7) (1q42.12)

Phenotype: OD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 101 Enhancers around

Promoter: 26 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.224634780G>A
GRCh37.p13 chr 1	NC_000001.10:g.224822482G>A

Gene: CNIH3, cornichon family AMPA receptor auxiliary protein 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNIH3 transcript variant 2	NM_001322302.1:c.	N/A	Intron Variant
CNIH3 transcript variant 3	NM_001322303.1:c.	N/A	Intron Variant
CNIH3 transcript variant 4	NM_001322304.1:c.	N/A	Intron Variant
CNIH3 transcript variant 5	NM_001322305.1:c.	N/A	Intron Variant
CNIH3 transcript variant 1	NM_152495.1:c.	N/A	Intron Variant
CNIH3 transcript variant 6	NR_136287.1:n.	N/A	Intron Variant
CNIH3 transcript variant 7	NR_136288.1:n.	N/A	Intron Variant
CNIH3 transcript variant 8	NR_136289.1:n.	N/A	Intron Variant
CNIH3 transcript variant 9	NR_136290.1:n.	N/A	Intron Variant
CNIH3 transcript variant 10	NR_136291.1:n.	N/A	Intron Variant
CNIH3 transcript variant 11	NR_136292.1:n.	N/A	Intron Variant
CNIH3 transcript variant 12	NR_136293.1:n.	N/A	Intron Variant
CNIH3 transcript variant 13	NR_136294.1:n.	N/A	Intron Variant
CNIH3 transcript variant 14	NR_136295.1:n.	N/A	Intron Variant
CNIH3 transcript variant 15	NR_136296.1:n.	N/A	Intron Variant
CNIH3 transcript variant 16	NR_136297.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.182	A=0.818
1000Genomes	American	Sub	694	G=0.370	A=0.630
1000Genomes	East Asian	Sub	1008	G=0.235	A=0.765
1000Genomes	Europe	Sub	1006	G=0.608	A=0.392
1000Genomes	Global	Study-wide	5008	G=0.361	A=0.639
1000Genomes	South Asian	Sub	978	G=0.480	A=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.552	A=0.448
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.409	A=0.590
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.546	A=0.454

PMID	Title	Author	Journal
26239289	Evidence of CNIH3 involvement in opioid dependence.	Nelson EC	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs10799590	4E-09	Opioid dependence	26239289

eQTL of rs10799590 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 rs10799590 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	224780347	224780450	E067	-42032
chr1	224780717	224780838	E067	-41644
chr1	224856778	224857029	E067	34296
chr1	224780717	224780838	E069	-41644
chr1	224780915	224781217	E069	-41265
chr1	224856778	224857029	E069	34296
chr1	224857579	224857690	E069	35097
chr1	224857770	224857830	E069	35288
chr1	224817844	224817966	E070	-4516
chr1	224819384	224819638	E070	-2844
chr1	224819665	224819766	E070	-2716
chr1	224819868	224819951	E070	-2531
chr1	224832330	224832684	E070	9848
chr1	224835232	224835511	E070	12750
chr1	224871804	224871953	E070	49322
chr1	224780347	224780450	E071	-42032
chr1	224780717	224780838	E071	-41644
chr1	224819384	224819638	E071	-2844
chr1	224819665	224819766	E071	-2716
chr1	224819868	224819951	E071	-2531
chr1	224820052	224820610	E071	-1872
chr1	224856778	224857029	E071	34296
chr1	224819868	224819951	E072	-2531
chr1	224856778	224857029	E072	34296
chr1	224857579	224857690	E072	35097
chr1	224802900	224802968	E073	-19514
chr1	224780347	224780450	E074	-42032
chr1	224780717	224780838	E074	-41644
chr1	224780915	224781217	E074	-41265
chr1	224856778	224857029	E074	34296
chr1	224857579	224857690	E074	35097
chr1	224857770	224857830	E074	35288
chr1	224775770	224775995	E081	-46487
chr1	224776063	224776609	E081	-45873
chr1	224776735	224777135	E081	-45347
chr1	224810464	224810641	E081	-11841
chr1	224810698	224810764	E081	-11718
chr1	224810864	224810966	E081	-11516
chr1	224811004	224811316	E081	-11166
chr1	224811370	224812331	E081	-10151
chr1	224812491	224812554	E081	-9928
chr1	224813424	224813474	E081	-9008
chr1	224813594	224813691	E081	-8791
chr1	224813839	224814055	E081	-8427
chr1	224814560	224814754	E081	-7728
chr1	224816403	224816462	E081	-6020
chr1	224817225	224817285	E081	-5197
chr1	224817844	224817966	E081	-4516
chr1	224819080	224819135	E081	-3347
chr1	224819384	224819638	E081	-2844
chr1	224819665	224819766	E081	-2716
chr1	224819868	224819951	E081	-2531
chr1	224820052	224820610	E081	-1872
chr1	224820734	224820956	E081	-1526
chr1	224821183	224821328	E081	-1154
chr1	224821475	224821525	E081	-957
chr1	224821533	224821758	E081	-724
chr1	224821821	224821940	E081	-542
chr1	224822353	224822416	E081	-66
chr1	224822545	224822617	E081	63
chr1	224822942	224823038	E081	460
chr1	224823040	224823385	E081	558
chr1	224825233	224825594	E081	2751
chr1	224825799	224825916	E081	3317
chr1	224827004	224827952	E081	4522
chr1	224827967	224828103	E081	5485
chr1	224828349	224828589	E081	5867
chr1	224828844	224829003	E081	6362
chr1	224835232	224835511	E081	12750
chr1	224837996	224838121	E081	15514
chr1	224838154	224838325	E081	15672
chr1	224853918	224854038	E081	31436
chr1	224854550	224854796	E081	32068
chr1	224854818	224854898	E081	32336
chr1	224856085	224856135	E081	33603
chr1	224856778	224857029	E081	34296
chr1	224860970	224861207	E081	38488
chr1	224861212	224861492	E081	38730
chr1	224871804	224871953	E081	49322
chr1	224776063	224776609	E082	-45873
chr1	224816403	224816462	E082	-6020
chr1	224817225	224817285	E082	-5197
chr1	224817844	224817966	E082	-4516
chr1	224819080	224819135	E082	-3347
chr1	224819384	224819638	E082	-2844
chr1	224819665	224819766	E082	-2716
chr1	224819868	224819951	E082	-2531
chr1	224820052	224820610	E082	-1872
chr1	224820734	224820956	E082	-1526
chr1	224821183	224821328	E082	-1154
chr1	224821475	224821525	E082	-957
chr1	224821533	224821758	E082	-724
chr1	224821821	224821940	E082	-542
chr1	224822353	224822416	E082	-66
chr1	224822545	224822617	E082	63
chr1	224825233	224825594	E082	2751
chr1	224827967	224828103	E082	5485
chr1	224837996	224838121	E082	15514
chr1	224838154	224838325	E082	15672
chr1	224860970	224861207	E082	38488
chr1	224861212	224861492	E082	38730

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	224803437	224805049	E067	-17433
chr1	224805514	224805767	E067	-16715
chr1	224805804	224805889	E067	-16593
chr1	224803437	224805049	E068	-17433
chr1	224803437	224805049	E069	-17433
chr1	224805348	224805467	E071	-17015
chr1	224805514	224805767	E071	-16715
chr1	224805804	224805889	E071	-16593
chr1	224806631	224806716	E071	-15766
chr1	224806772	224806853	E071	-15629
chr1	224803437	224805049	E072	-17433
chr1	224805129	224805323	E072	-17159
chr1	224805348	224805467	E072	-17015
chr1	224805514	224805767	E072	-16715
chr1	224805804	224805889	E072	-16593
chr1	224807430	224807470	E072	-15012
chr1	224807492	224807574	E072	-14908
chr1	224805348	224805467	E073	-17015
chr1	224805514	224805767	E073	-16715
chr1	224805804	224805889	E073	-16593
chr1	224806631	224806716	E082	-15766
chr1	224806772	224806853	E082	-15629
chr1	224807430	224807470	E082	-15012
chr1	224807492	224807574	E082	-14908
chr1	224807958	224808008	E082	-14474
chr1	224808628	224808713	E082	-13769