rs11165257

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

SLC44A3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0017 (514/29968,GnomAD)
T=0027 (809/29118,TOPMED)
T=0020 (98/5008,1000G)
T=0002 (6/3854,ALSPAC)
T=0001 (5/3708,TWINSUK)

Position: chr1:94836579 (GRCh38.p7) (1p21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 176 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.94836579G>T
GRCh37.p13 chr 1	NC_000001.10:g.95302135G>T

Gene: SLC44A3, solute carrier family 44 member 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC44A3 transcript variant 1	NM_001114106.2:c.	N/A	Intron Variant
SLC44A3 transcript variant 3	NM_001258340.1:c.	N/A	Intron Variant
SLC44A3 transcript variant 4	NM_001258341.1:c.	N/A	Intron Variant
SLC44A3 transcript variant 5	NM_001258342.1:c.	N/A	Intron Variant
SLC44A3 transcript variant 6	NM_001258343.1:c.	N/A	Intron Variant
SLC44A3 transcript variant 7	NM_001301079.1:c.	N/A	Intron Variant
SLC44A3 transcript variant 2	NM_152369.4:c.	N/A	Intron Variant
SLC44A3 transcript variant X1	XM_005270440.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X3	XM_005270441.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X5	XM_005270442.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X8	XM_011540632.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X8	XM_011540633.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X13	XM_011540635.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X14	XM_011540636.2:c.	N/A	Intron Variant
SLC44A3 transcript variant X2	XM_017000262.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X4	XM_017000263.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X6	XM_017000264.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X7	XM_017000265.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X12	XM_017000266.1:c.	N/A	Intron Variant
SLC44A3 transcript variant X10	XR_001736960.1:n.	N/A	Intron Variant
SLC44A3 transcript variant X15	XR_001736961.1:n.	N/A	Intron Variant
SLC44A3 transcript variant X16	XR_001736962.1:n.	N/A	Intron Variant
SLC44A3 transcript variant X11	XR_946543.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.930	T=0.070
1000Genomes	American	Sub	694	G=0.990	T=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	T=0.000
1000Genomes	Europe	Sub	1006	G=0.998	T=0.002
1000Genomes	Global	Study-wide	5008	G=0.980	T=0.020
1000Genomes	South Asian	Sub	978	G=1.000	T=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.998	T=0.002
The Genome Aggregation Database	African	Sub	8718	G=0.942	T=0.058
The Genome Aggregation Database	American	Sub	838	G=1.000	T=0.000
The Genome Aggregation Database	East Asian	Sub	1622	G=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18488	G=0.999	T=0.000
The Genome Aggregation Database	Global	Study-wide	29968	G=0.982	T=0.017
The Genome Aggregation Database	Other	Sub	302	G=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.972	T=0.027
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.999	T=0.001

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
rs11165257	0.000274	alcohol dependence	20201924

eQTL of rs11165257 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 rs11165257 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	95258066	95259213	E067	-42922
chr1	95266770	95266855	E067	-35280
chr1	95266882	95266952	E067	-35183
chr1	95267400	95268169	E067	-33966
chr1	95268227	95268317	E067	-33818
chr1	95268757	95269820	E067	-32315
chr1	95270096	95270337	E067	-31798
chr1	95272016	95272361	E067	-29774
chr1	95272384	95272557	E067	-29578
chr1	95293095	95293208	E067	-8927
chr1	95319849	95320916	E067	17714
chr1	95325396	95325504	E067	23261
chr1	95331624	95331705	E067	29489
chr1	95331829	95332323	E067	29694
chr1	95332563	95332832	E067	30428
chr1	95332880	95333041	E067	30745
chr1	95338479	95339112	E067	36344
chr1	95339155	95339787	E067	37020
chr1	95340137	95340191	E067	38002
chr1	95340216	95340273	E067	38081
chr1	95349203	95349628	E067	47068
chr1	95349643	95350415	E067	47508
chr1	95257711	95257761	E068	-44374
chr1	95258066	95259213	E068	-42922
chr1	95266770	95266855	E068	-35280
chr1	95266882	95266952	E068	-35183
chr1	95268227	95268317	E068	-33818
chr1	95268757	95269820	E068	-32315
chr1	95270096	95270337	E068	-31798
chr1	95271344	95271435	E068	-30700
chr1	95271789	95271910	E068	-30225
chr1	95272016	95272361	E068	-29774
chr1	95320941	95321091	E068	18806
chr1	95321173	95321321	E068	19038
chr1	95325396	95325504	E068	23261
chr1	95328112	95328168	E068	25977
chr1	95328238	95330026	E068	26103
chr1	95330071	95331347	E068	27936
chr1	95331624	95331705	E068	29489
chr1	95331829	95332323	E068	29694
chr1	95338263	95338313	E068	36128
chr1	95338479	95339112	E068	36344
chr1	95339155	95339787	E068	37020
chr1	95340137	95340191	E068	38002
chr1	95340216	95340273	E068	38081
chr1	95348849	95348904	E068	46714
chr1	95349203	95349628	E068	47068
chr1	95350931	95351067	E068	48796
chr1	95258066	95259213	E069	-42922
chr1	95268227	95268317	E069	-33818
chr1	95268757	95269820	E069	-32315
chr1	95270096	95270337	E069	-31798
chr1	95271789	95271910	E069	-30225
chr1	95272016	95272361	E069	-29774
chr1	95272384	95272557	E069	-29578
chr1	95319849	95320916	E069	17714
chr1	95320941	95321091	E069	18806
chr1	95321173	95321321	E069	19038
chr1	95324819	95325097	E069	22684
chr1	95325396	95325504	E069	23261
chr1	95330071	95331347	E069	27936
chr1	95331624	95331705	E069	29489
chr1	95331829	95332323	E069	29694
chr1	95332563	95332832	E069	30428
chr1	95332880	95333041	E069	30745
chr1	95340137	95340191	E069	38002
chr1	95340216	95340273	E069	38081
chr1	95348072	95348288	E069	45937
chr1	95349203	95349628	E069	47068
chr1	95349643	95350415	E069	47508
chr1	95268227	95268317	E070	-33818
chr1	95268757	95269820	E070	-32315
chr1	95272016	95272361	E070	-29774
chr1	95272384	95272557	E070	-29578
chr1	95272652	95272709	E070	-29426
chr1	95272724	95272795	E070	-29340
chr1	95320941	95321091	E070	18806
chr1	95321173	95321321	E070	19038
chr1	95325396	95325504	E070	23261
chr1	95328238	95330026	E070	26103
chr1	95330071	95331347	E070	27936
chr1	95331624	95331705	E070	29489
chr1	95331829	95332323	E070	29694
chr1	95339155	95339787	E070	37020
chr1	95340137	95340191	E070	38002
chr1	95340216	95340273	E070	38081
chr1	95349643	95350415	E070	47508
chr1	95257711	95257761	E071	-44374
chr1	95258066	95259213	E071	-42922
chr1	95263568	95263617	E071	-38518
chr1	95266493	95266612	E071	-35523
chr1	95266770	95266855	E071	-35280
chr1	95266882	95266952	E071	-35183
chr1	95268227	95268317	E071	-33818
chr1	95268757	95269820	E071	-32315
chr1	95270096	95270337	E071	-31798
chr1	95271344	95271435	E071	-30700
chr1	95271444	95271763	E071	-30372
chr1	95271789	95271910	E071	-30225
chr1	95272016	95272361	E071	-29774
chr1	95272384	95272557	E071	-29578
chr1	95293095	95293208	E071	-8927
chr1	95320941	95321091	E071	18806
chr1	95321173	95321321	E071	19038
chr1	95330071	95331347	E071	27936
chr1	95331624	95331705	E071	29489
chr1	95331829	95332323	E071	29694
chr1	95332563	95332832	E071	30428
chr1	95332880	95333041	E071	30745
chr1	95338263	95338313	E071	36128
chr1	95340137	95340191	E071	38002
chr1	95348849	95348904	E071	46714
chr1	95349643	95350415	E071	47508
chr1	95257711	95257761	E072	-44374
chr1	95258066	95259213	E072	-42922
chr1	95268227	95268317	E072	-33818
chr1	95268757	95269820	E072	-32315
chr1	95270096	95270337	E072	-31798
chr1	95271444	95271763	E072	-30372
chr1	95271789	95271910	E072	-30225
chr1	95272016	95272361	E072	-29774
chr1	95272384	95272557	E072	-29578
chr1	95319849	95320916	E072	17714
chr1	95320941	95321091	E072	18806
chr1	95325396	95325504	E072	23261
chr1	95328238	95330026	E072	26103
chr1	95330071	95331347	E072	27936
chr1	95331624	95331705	E072	29489
chr1	95331829	95332323	E072	29694
chr1	95338263	95338313	E072	36128
chr1	95338479	95339112	E072	36344
chr1	95340137	95340191	E072	38002
chr1	95347893	95347943	E072	45758
chr1	95348072	95348288	E072	45937
chr1	95348849	95348904	E072	46714
chr1	95349203	95349628	E072	47068
chr1	95257711	95257761	E073	-44374
chr1	95258066	95259213	E073	-42922
chr1	95267400	95268169	E073	-33966
chr1	95268227	95268317	E073	-33818
chr1	95268757	95269820	E073	-32315
chr1	95270096	95270337	E073	-31798
chr1	95320941	95321091	E073	18806
chr1	95325396	95325504	E073	23261
chr1	95328238	95330026	E073	26103
chr1	95330071	95331347	E073	27936
chr1	95331624	95331705	E073	29489
chr1	95331829	95332323	E073	29694
chr1	95338479	95339112	E073	36344
chr1	95339155	95339787	E073	37020
chr1	95340137	95340191	E073	38002
chr1	95258066	95259213	E074	-42922
chr1	95268227	95268317	E074	-33818
chr1	95270096	95270337	E074	-31798
chr1	95330071	95331347	E074	27936
chr1	95331624	95331705	E074	29489
chr1	95331829	95332323	E074	29694
chr1	95338263	95338313	E074	36128
chr1	95338479	95339112	E074	36344
chr1	95339155	95339787	E074	37020
chr1	95340137	95340191	E074	38002
chr1	95349203	95349628	E074	47068
chr1	95349643	95350415	E074	47508
chr1	95350931	95351067	E074	48796
chr1	95271444	95271763	E081	-30372
chr1	95271789	95271910	E081	-30225
chr1	95272016	95272361	E081	-29774
chr1	95272384	95272557	E081	-29578
chr1	95328238	95330026	E081	26103
chr1	95330071	95331347	E081	27936
chr1	95340137	95340191	E081	38002
chr1	95349643	95350415	E081	47508
chr1	95267400	95268169	E082	-33966
chr1	95272016	95272361	E082	-29774
chr1	95272384	95272557	E082	-29578
chr1	95328238	95330026	E082	26103

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	95285185	95286322	E067	-15813
chr1	95286347	95287886	E067	-14249
chr1	95285185	95286322	E068	-15813
chr1	95285185	95286322	E069	-15813
chr1	95285185	95286322	E070	-15813
chr1	95285185	95286322	E071	-15813
chr1	95285185	95286322	E072	-15813
chr1	95285185	95286322	E073	-15813
chr1	95285185	95286322	E074	-15813
chr1	95285185	95286322	E082	-15813