rs16846221

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

SLC4A10 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0067 (2012/29944,GnomAD)
T=0066 (1934/29118,TOPMED)
T=0141 (706/5008,1000G)
T=0015 (57/3854,ALSPAC)
T=0016 (61/3708,TWINSUK)

Position: chr2:161963710 (GRCh38.p7) (2q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 69 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.161963710G>T
GRCh37.p13 chr 2	NC_000002.11:g.162820220G>T
SLC4A10 RefSeqGene	NG_021401.1:g.344376G>T

Gene: SLC4A10, solute carrier family 4 member 10(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC4A10 transcript variant 1	NM_001178015.1:c.	N/A	Intron Variant
SLC4A10 transcript variant 3	NM_001178016.1:c.	N/A	Intron Variant
SLC4A10 transcript variant 2	NM_022058.3:c.	N/A	Intron Variant
SLC4A10 transcript variant X6	XM_005246694.4:c.	N/A	Intron Variant
SLC4A10 transcript variant X15	XM_005246695.4:c.	N/A	Intron Variant
SLC4A10 transcript variant X1	XM_011511508.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X2	XM_011511509.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X4	XM_011511510.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X5	XM_011511511.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X6	XM_011511512.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X4	XM_011511513.2:c.	N/A	Intron Variant
SLC4A10 transcript variant X3	XM_017004541.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X7	XM_017004542.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X8	XM_017004543.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X9	XM_017004544.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X12	XM_017004545.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X8	XM_017004546.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X14	XM_017004547.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X16	XM_017004548.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X17	XM_017004549.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X18	XM_017004550.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X9	XM_017004551.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X20	XM_017004552.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X21	XM_017004553.1:c.	N/A	Intron Variant
SLC4A10 transcript variant X11	XM_017004554.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.855	T=0.145
1000Genomes	American	Sub	694	G=0.990	T=0.010
1000Genomes	East Asian	Sub	1008	G=0.754	T=0.246
1000Genomes	Europe	Sub	1006	G=0.974	T=0.026
1000Genomes	Global	Study-wide	5008	G=0.859	T=0.141
1000Genomes	South Asian	Sub	978	G=0.760	T=0.240
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.985	T=0.015
The Genome Aggregation Database	African	Sub	8718	G=0.883	T=0.117
The Genome Aggregation Database	American	Sub	838	G=0.970	T=0.030
The Genome Aggregation Database	East Asian	Sub	1616	G=0.724	T=0.276
The Genome Aggregation Database	Europe	Sub	18470	G=0.972	T=0.027
The Genome Aggregation Database	Global	Study-wide	29944	G=0.932	T=0.067
The Genome Aggregation Database	Other	Sub	302	G=0.950	T=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.933	T=0.066
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.984	T=0.016

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs16846221	0.00049	alcohol dependence	20201924

eQTL of rs16846221 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 rs16846221 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	162854429	162854485	E067	34209
chr2	162854760	162855399	E067	34540
chr2	162858246	162858347	E069	38026
chr2	162858540	162858638	E069	38320
chr2	162858683	162859181	E069	38463
chr2	162804334	162804740	E070	-15480
chr2	162852137	162852410	E070	31917
chr2	162858540	162858638	E070	38320
chr2	162858683	162859181	E070	38463
chr2	162858683	162859181	E074	38463
chr2	162859215	162859791	E074	38995
chr2	162869238	162869476	E074	49018
chr2	162869795	162869864	E074	49575
chr2	162803171	162803344	E081	-16876
chr2	162803419	162803506	E081	-16714
chr2	162804058	162804187	E081	-16033
chr2	162804334	162804740	E081	-15480
chr2	162804858	162804942	E081	-15278
chr2	162809215	162809692	E081	-10528
chr2	162810203	162811010	E081	-9210
chr2	162823740	162823841	E081	3520
chr2	162825410	162825624	E081	5190
chr2	162825757	162826032	E081	5537
chr2	162826224	162826289	E081	6004
chr2	162848647	162848785	E081	28427
chr2	162848883	162848950	E081	28663
chr2	162849611	162850030	E081	29391
chr2	162852137	162852410	E081	31917
chr2	162852411	162852490	E081	32191
chr2	162852622	162852672	E081	32402
chr2	162854429	162854485	E081	34209
chr2	162854760	162855399	E081	34540
chr2	162855474	162855615	E081	35254
chr2	162855823	162856342	E081	35603
chr2	162856497	162856779	E081	36277
chr2	162856847	162857521	E081	36627
chr2	162858246	162858347	E081	38026
chr2	162858540	162858638	E081	38320
chr2	162858683	162859181	E081	38463
chr2	162859215	162859791	E081	38995
chr2	162860043	162860093	E081	39823
chr2	162860692	162860803	E081	40472
chr2	162861086	162861397	E081	40866
chr2	162861484	162861727	E081	41264
chr2	162865753	162865813	E081	45533
chr2	162803419	162803506	E082	-16714
chr2	162804058	162804187	E082	-16033
chr2	162804334	162804740	E082	-15480
chr2	162804858	162804942	E082	-15278
chr2	162805115	162805208	E082	-15012
chr2	162825410	162825624	E082	5190
chr2	162825757	162826032	E082	5537
chr2	162826224	162826289	E082	6004
chr2	162848647	162848785	E082	28427
chr2	162848883	162848950	E082	28663
chr2	162852411	162852490	E082	32191
chr2	162852622	162852672	E082	32402
chr2	162854429	162854485	E082	34209
chr2	162854760	162855399	E082	34540
chr2	162855474	162855615	E082	35254
chr2	162855823	162856342	E082	35603
chr2	162856497	162856779	E082	36277
chr2	162856847	162857521	E082	36627
chr2	162858246	162858347	E082	38026
chr2	162858540	162858638	E082	38320
chr2	162858683	162859181	E082	38463
chr2	162859215	162859791	E082	38995
chr2	162860043	162860093	E082	39823
chr2	162860692	162860803	E082	40472