rs2267032

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SMARCB1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0300 (8997/29952,GnomAD)
A==0358 (10437/29116,TOPMED)
A==0394 (1971/5008,1000G)
A==0188 (723/3854,ALSPAC)
A==0188 (697/3708,TWINSUK)

Position: chr22:23806086 (GRCh38.p7) (22q11.23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 375 Enhancers around

Promoter: 27 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.23806086A>G
GRCh37.p13 chr 22	NC_000022.10:g.24148273A>G
SMARCB1 RefSeqGene	LRG_520
GRCh38.p7 chr 22 alt locus HSCHR22_1_CTG7	NT_187633.1:g.42448A>G

Gene: SMARCB1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SMARCB1 transcript variant 2	NM_001007468.2:c.	N/A	Intron Variant
SMARCB1 transcript variant 3	NM_001317946.1:c.	N/A	Intron Variant
SMARCB1 transcript variant 1	NM_003073.4:c.	N/A	Intron Variant
SMARCB1 transcript variant X1	XM_011530345.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.601	G=0.399
1000Genomes	American	Sub	694	A=0.220	G=0.780
1000Genomes	East Asian	Sub	1008	A=0.357	G=0.643
1000Genomes	Europe	Sub	1006	A=0.186	G=0.814
1000Genomes	Global	Study-wide	5008	A=0.394	G=0.606
1000Genomes	South Asian	Sub	978	A=0.480	G=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.188	G=0.812
The Genome Aggregation Database	African	Sub	8710	A=0.500	G=0.500
The Genome Aggregation Database	American	Sub	838	A=0.240	G=0.760
The Genome Aggregation Database	East Asian	Sub	1614	A=0.397	G=0.603
The Genome Aggregation Database	Europe	Sub	18488	A=0.202	G=0.797
The Genome Aggregation Database	Global	Study-wide	29952	A=0.300	G=0.699
The Genome Aggregation Database	Other	Sub	302	A=0.210	G=0.790
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.358	G=0.641
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.188	G=0.812

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
24556940	Genetic variant in SWI/SNF complexes influences hepatocellular carcinoma risk: a new clue for the contribution of chromatin remodeling in carcinogenesis.	Zhong R	Sci Rep

P-Value

SNP ID	p-value	Traits	Study
rs2267032	0.00058	alcohol dependence(early age of onset)	20201924
rs2267032	0.00088	alcohol dependence	20201924

eQTL of rs2267032 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr22:24148273	SMARCB1	ENSG00000099956.13	A>G	1.3244e-7	19123	Cerebellum
Chr22:24148273	VPREB3	ENSG00000128218.7	A>G	6.5066e-10	51618	Cortex
Chr22:24148273	VPREB3	ENSG00000128218.7	A>G	1.7131e-8	51618	Anterior_cingulate_cortex

meQTL of rs2267032 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 )
chr22	24104735	24106360	E067	-41913
chr22	24107792	24108020	E067	-40253
chr22	24108031	24108370	E067	-39903
chr22	24108397	24108499	E067	-39774
chr22	24111316	24111523	E067	-36750
chr22	24111572	24111750	E067	-36523
chr22	24111760	24112069	E067	-36204
chr22	24122843	24122926	E067	-25347
chr22	24122962	24123022	E067	-25251
chr22	24123067	24123117	E067	-25156
chr22	24123308	24124259	E067	-24014
chr22	24130460	24130538	E067	-17735
chr22	24131440	24131561	E067	-16712
chr22	24131663	24131857	E067	-16416
chr22	24131871	24132002	E067	-16271
chr22	24132027	24132167	E067	-16106
chr22	24132202	24132432	E067	-15841
chr22	24132473	24132569	E067	-15704
chr22	24146998	24147317	E067	-956
chr22	24147382	24147454	E067	-819
chr22	24164254	24164304	E067	15981
chr22	24164502	24164830	E067	16229
chr22	24164904	24165118	E067	16631
chr22	24176461	24176509	E067	28188
chr22	24176651	24176729	E067	28378
chr22	24176821	24176918	E067	28548
chr22	24176963	24177630	E067	28690
chr22	24177644	24177761	E067	29371
chr22	24177817	24177936	E067	29544
chr22	24106369	24106630	E068	-41643
chr22	24106654	24106744	E068	-41529
chr22	24106756	24106923	E068	-41350
chr22	24107003	24107057	E068	-41216
chr22	24107113	24107197	E068	-41076
chr22	24107302	24107727	E068	-40546
chr22	24107792	24108020	E068	-40253
chr22	24113228	24113591	E068	-34682
chr22	24122605	24122655	E068	-25618
chr22	24122843	24122926	E068	-25347
chr22	24122962	24123022	E068	-25251
chr22	24123067	24123117	E068	-25156
chr22	24123308	24124259	E068	-24014
chr22	24130460	24130538	E068	-17735
chr22	24130848	24130904	E068	-17369
chr22	24130917	24130991	E068	-17282
chr22	24131440	24131561	E068	-16712
chr22	24131663	24131857	E068	-16416
chr22	24131871	24132002	E068	-16271
chr22	24132027	24132167	E068	-16106
chr22	24132202	24132432	E068	-15841
chr22	24132473	24132569	E068	-15704
chr22	24132967	24133085	E068	-15188
chr22	24164254	24164304	E068	15981
chr22	24164502	24164830	E068	16229
chr22	24170972	24171140	E068	22699
chr22	24171298	24171469	E068	23025
chr22	24171534	24171678	E068	23261
chr22	24175830	24175906	E068	27557
chr22	24175944	24176454	E068	27671
chr22	24176461	24176509	E068	28188
chr22	24176651	24176729	E068	28378
chr22	24176821	24176918	E068	28548
chr22	24176963	24177630	E068	28690
chr22	24177644	24177761	E068	29371
chr22	24177817	24177936	E068	29544
chr22	24186514	24187069	E068	38241
chr22	24187666	24188271	E068	39393
chr22	24188278	24188357	E068	40005
chr22	24188411	24189377	E068	40138
chr22	24191170	24192176	E068	42897
chr22	24104735	24106360	E069	-41913
chr22	24106369	24106630	E069	-41643
chr22	24106654	24106744	E069	-41529
chr22	24106756	24106923	E069	-41350
chr22	24107302	24107727	E069	-40546
chr22	24111316	24111523	E069	-36750
chr22	24111572	24111750	E069	-36523
chr22	24122605	24122655	E069	-25618
chr22	24122843	24122926	E069	-25347
chr22	24122962	24123022	E069	-25251
chr22	24123067	24123117	E069	-25156
chr22	24123308	24124259	E069	-24014
chr22	24130848	24130904	E069	-17369
chr22	24130917	24130991	E069	-17282
chr22	24131440	24131561	E069	-16712
chr22	24131663	24131857	E069	-16416
chr22	24131871	24132002	E069	-16271
chr22	24132027	24132167	E069	-16106
chr22	24132202	24132432	E069	-15841
chr22	24132473	24132569	E069	-15704
chr22	24157813	24158044	E069	9540
chr22	24158089	24158192	E069	9816
chr22	24158226	24159753	E069	9953
chr22	24164254	24164304	E069	15981
chr22	24164502	24164830	E069	16229
chr22	24164904	24165118	E069	16631
chr22	24165254	24165365	E069	16981
chr22	24170754	24170810	E069	22481
chr22	24170972	24171140	E069	22699
chr22	24171298	24171469	E069	23025
chr22	24171534	24171678	E069	23261
chr22	24171715	24171796	E069	23442
chr22	24174004	24174281	E069	25731
chr22	24174349	24174952	E069	26076
chr22	24175105	24175211	E069	26832
chr22	24175287	24175424	E069	27014
chr22	24175479	24175667	E069	27206
chr22	24175830	24175906	E069	27557
chr22	24175944	24176454	E069	27671
chr22	24176461	24176509	E069	28188
chr22	24176651	24176729	E069	28378
chr22	24176821	24176918	E069	28548
chr22	24176963	24177630	E069	28690
chr22	24177644	24177761	E069	29371
chr22	24177817	24177936	E069	29544
chr22	24188411	24189377	E069	40138
chr22	24191170	24192176	E069	42897
chr22	24106369	24106630	E070	-41643
chr22	24106654	24106744	E070	-41529
chr22	24106756	24106923	E070	-41350
chr22	24111316	24111523	E070	-36750
chr22	24111572	24111750	E070	-36523
chr22	24130848	24130904	E070	-17369
chr22	24130917	24130991	E070	-17282
chr22	24131440	24131561	E070	-16712
chr22	24131663	24131857	E070	-16416
chr22	24131871	24132002	E070	-16271
chr22	24132027	24132167	E070	-16106
chr22	24132202	24132432	E070	-15841
chr22	24132473	24132569	E070	-15704
chr22	24183617	24184737	E070	35344
chr22	24184797	24184960	E070	36524
chr22	24184978	24185207	E070	36705
chr22	24188411	24189377	E070	40138
chr22	24189610	24189660	E070	41337
chr22	24189705	24189758	E070	41432
chr22	24189766	24189822	E070	41493
chr22	24190016	24190102	E070	41743
chr22	24190191	24190965	E070	41918
chr22	24191170	24192176	E070	42897
chr22	24104735	24106360	E071	-41913
chr22	24106369	24106630	E071	-41643
chr22	24106654	24106744	E071	-41529
chr22	24106756	24106923	E071	-41350
chr22	24107302	24107727	E071	-40546
chr22	24107792	24108020	E071	-40253
chr22	24111316	24111523	E071	-36750
chr22	24111572	24111750	E071	-36523
chr22	24113228	24113591	E071	-34682
chr22	24120134	24120230	E071	-28043
chr22	24120254	24120337	E071	-27936
chr22	24122528	24122578	E071	-25695
chr22	24122605	24122655	E071	-25618
chr22	24122843	24122926	E071	-25347
chr22	24122962	24123022	E071	-25251
chr22	24123067	24123117	E071	-25156
chr22	24123308	24124259	E071	-24014
chr22	24124425	24124475	E071	-23798
chr22	24124478	24124933	E071	-23340
chr22	24130460	24130538	E071	-17735
chr22	24130848	24130904	E071	-17369
chr22	24130917	24130991	E071	-17282
chr22	24131440	24131561	E071	-16712
chr22	24131663	24131857	E071	-16416
chr22	24131871	24132002	E071	-16271
chr22	24132027	24132167	E071	-16106
chr22	24132202	24132432	E071	-15841
chr22	24146998	24147317	E071	-956
chr22	24147382	24147454	E071	-819
chr22	24157813	24158044	E071	9540
chr22	24158089	24158192	E071	9816
chr22	24158226	24159753	E071	9953
chr22	24164502	24164830	E071	16229
chr22	24164904	24165118	E071	16631
chr22	24165254	24165365	E071	16981
chr22	24170972	24171140	E071	22699
chr22	24171298	24171469	E071	23025
chr22	24175105	24175211	E071	26832
chr22	24175287	24175424	E071	27014
chr22	24175479	24175667	E071	27206
chr22	24175830	24175906	E071	27557
chr22	24175944	24176454	E071	27671
chr22	24176461	24176509	E071	28188
chr22	24176651	24176729	E071	28378
chr22	24176821	24176918	E071	28548
chr22	24176963	24177630	E071	28690
chr22	24177644	24177761	E071	29371
chr22	24177817	24177936	E071	29544
chr22	24178007	24178108	E071	29734
chr22	24178156	24178345	E071	29883
chr22	24187128	24187489	E071	38855
chr22	24187666	24188271	E071	39393
chr22	24188278	24188357	E071	40005
chr22	24188411	24189377	E071	40138
chr22	24191170	24192176	E071	42897
chr22	24104735	24106360	E072	-41913
chr22	24106369	24106630	E072	-41643
chr22	24106654	24106744	E072	-41529
chr22	24111316	24111523	E072	-36750
chr22	24111572	24111750	E072	-36523
chr22	24111760	24112069	E072	-36204
chr22	24122843	24122926	E072	-25347
chr22	24123308	24124259	E072	-24014
chr22	24124425	24124475	E072	-23798
chr22	24124478	24124933	E072	-23340
chr22	24130460	24130538	E072	-17735
chr22	24130848	24130904	E072	-17369
chr22	24130917	24130991	E072	-17282
chr22	24131440	24131561	E072	-16712
chr22	24131663	24131857	E072	-16416
chr22	24131871	24132002	E072	-16271
chr22	24132027	24132167	E072	-16106
chr22	24132202	24132432	E072	-15841
chr22	24146998	24147317	E072	-956
chr22	24147382	24147454	E072	-819
chr22	24157813	24158044	E072	9540
chr22	24158089	24158192	E072	9816
chr22	24158226	24159753	E072	9953
chr22	24164502	24164830	E072	16229
chr22	24164904	24165118	E072	16631
chr22	24165254	24165365	E072	16981
chr22	24165509	24165946	E072	17236
chr22	24166046	24166324	E072	17773
chr22	24170754	24170810	E072	22481
chr22	24170972	24171140	E072	22699
chr22	24171298	24171469	E072	23025
chr22	24171534	24171678	E072	23261
chr22	24171715	24171796	E072	23442
chr22	24171876	24171955	E072	23603
chr22	24174004	24174281	E072	25731
chr22	24174349	24174952	E072	26076
chr22	24175105	24175211	E072	26832
chr22	24175287	24175424	E072	27014
chr22	24175479	24175667	E072	27206
chr22	24175830	24175906	E072	27557
chr22	24175944	24176454	E072	27671
chr22	24176461	24176509	E072	28188
chr22	24176651	24176729	E072	28378
chr22	24176821	24176918	E072	28548
chr22	24176963	24177630	E072	28690
chr22	24177644	24177761	E072	29371
chr22	24177817	24177936	E072	29544
chr22	24186514	24187069	E072	38241
chr22	24187128	24187489	E072	38855
chr22	24188278	24188357	E072	40005
chr22	24188411	24189377	E072	40138
chr22	24191170	24192176	E072	42897
chr22	24106369	24106630	E073	-41643
chr22	24106654	24106744	E073	-41529
chr22	24106756	24106923	E073	-41350
chr22	24107003	24107057	E073	-41216
chr22	24107113	24107197	E073	-41076
chr22	24107302	24107727	E073	-40546
chr22	24107792	24108020	E073	-40253
chr22	24108031	24108370	E073	-39903
chr22	24108397	24108499	E073	-39774
chr22	24108516	24108605	E073	-39668
chr22	24111316	24111523	E073	-36750
chr22	24111572	24111750	E073	-36523
chr22	24111760	24112069	E073	-36204
chr22	24122962	24123022	E073	-25251
chr22	24123067	24123117	E073	-25156
chr22	24123308	24124259	E073	-24014
chr22	24127701	24127972	E073	-20301
chr22	24130848	24130904	E073	-17369
chr22	24130917	24130991	E073	-17282
chr22	24131440	24131561	E073	-16712
chr22	24131663	24131857	E073	-16416
chr22	24131871	24132002	E073	-16271
chr22	24132027	24132167	E073	-16106
chr22	24132202	24132432	E073	-15841
chr22	24157813	24158044	E073	9540
chr22	24158089	24158192	E073	9816
chr22	24164254	24164304	E073	15981
chr22	24164502	24164830	E073	16229
chr22	24164904	24165118	E073	16631
chr22	24171298	24171469	E073	23025
chr22	24171534	24171678	E073	23261
chr22	24171715	24171796	E073	23442
chr22	24174349	24174952	E073	26076
chr22	24175105	24175211	E073	26832
chr22	24175287	24175424	E073	27014
chr22	24175479	24175667	E073	27206
chr22	24175830	24175906	E073	27557
chr22	24175944	24176454	E073	27671
chr22	24176461	24176509	E073	28188
chr22	24176651	24176729	E073	28378
chr22	24176821	24176918	E073	28548
chr22	24176963	24177630	E073	28690
chr22	24177644	24177761	E073	29371
chr22	24177817	24177936	E073	29544
chr22	24178007	24178108	E073	29734
chr22	24178156	24178345	E073	29883
chr22	24178370	24178979	E073	30097
chr22	24188411	24189377	E073	40138
chr22	24111316	24111523	E074	-36750
chr22	24111572	24111750	E074	-36523
chr22	24111760	24112069	E074	-36204
chr22	24113228	24113591	E074	-34682
chr22	24122528	24122578	E074	-25695
chr22	24122605	24122655	E074	-25618
chr22	24122843	24122926	E074	-25347
chr22	24122962	24123022	E074	-25251
chr22	24123067	24123117	E074	-25156
chr22	24123308	24124259	E074	-24014
chr22	24124425	24124475	E074	-23798
chr22	24130460	24130538	E074	-17735
chr22	24130848	24130904	E074	-17369
chr22	24130917	24130991	E074	-17282
chr22	24131440	24131561	E074	-16712
chr22	24131663	24131857	E074	-16416
chr22	24131871	24132002	E074	-16271
chr22	24132027	24132167	E074	-16106
chr22	24132202	24132432	E074	-15841
chr22	24170754	24170810	E074	22481
chr22	24170972	24171140	E074	22699
chr22	24171298	24171469	E074	23025
chr22	24171534	24171678	E074	23261
chr22	24171715	24171796	E074	23442
chr22	24175479	24175667	E074	27206
chr22	24175830	24175906	E074	27557
chr22	24175944	24176454	E074	27671
chr22	24176461	24176509	E074	28188
chr22	24176651	24176729	E074	28378
chr22	24176821	24176918	E074	28548
chr22	24176963	24177630	E074	28690
chr22	24177644	24177761	E074	29371
chr22	24177817	24177936	E074	29544
chr22	24178007	24178108	E074	29734
chr22	24178156	24178345	E074	29883
chr22	24186514	24187069	E074	38241
chr22	24188411	24189377	E074	40138
chr22	24189610	24189660	E074	41337
chr22	24189705	24189758	E074	41432
chr22	24191170	24192176	E074	42897
chr22	24104735	24106360	E081	-41913
chr22	24111316	24111523	E081	-36750
chr22	24111572	24111750	E081	-36523
chr22	24116207	24116479	E081	-31794
chr22	24116508	24116680	E081	-31593
chr22	24116683	24116823	E081	-31450
chr22	24130848	24130904	E081	-17369
chr22	24130917	24130991	E081	-17282
chr22	24131440	24131561	E081	-16712
chr22	24131663	24131857	E081	-16416
chr22	24131871	24132002	E081	-16271
chr22	24132027	24132167	E081	-16106
chr22	24132202	24132432	E081	-15841
chr22	24132473	24132569	E081	-15704
chr22	24133151	24134384	E081	-13889
chr22	24157813	24158044	E081	9540
chr22	24158089	24158192	E081	9816
chr22	24158226	24159753	E081	9953
chr22	24173621	24173752	E081	25348
chr22	24173797	24173894	E081	25524
chr22	24179096	24179171	E081	30823
chr22	24188411	24189377	E081	40138
chr22	24189610	24189660	E081	41337
chr22	24189705	24189758	E081	41432
chr22	24189766	24189822	E081	41493
chr22	24190016	24190102	E081	41743
chr22	24190191	24190965	E081	41918
chr22	24191170	24192176	E081	42897
chr22	24104735	24106360	E082	-41913
chr22	24106369	24106630	E082	-41643
chr22	24111316	24111523	E082	-36750
chr22	24116207	24116479	E082	-31794
chr22	24131440	24131561	E082	-16712
chr22	24131663	24131857	E082	-16416
chr22	24133151	24134384	E082	-13889
chr22	24157813	24158044	E082	9540
chr22	24158089	24158192	E082	9816
chr22	24158226	24159753	E082	9953
chr22	24179096	24179171	E082	30823
chr22	24188411	24189377	E082	40138

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	24108836	24111069	E067	-37204
chr22	24128387	24130388	E067	-17885
chr22	24179219	24182229	E067	30946
chr22	24108836	24111069	E068	-37204
chr22	24128387	24130388	E068	-17885
chr22	24179219	24182229	E068	30946
chr22	24108836	24111069	E069	-37204
chr22	24128387	24130388	E069	-17885
chr22	24108836	24111069	E070	-37204
chr22	24128387	24130388	E070	-17885
chr22	24179219	24182229	E070	30946
chr22	24108836	24111069	E071	-37204
chr22	24128387	24130388	E071	-17885
chr22	24179219	24182229	E071	30946
chr22	24108836	24111069	E072	-37204
chr22	24128387	24130388	E072	-17885
chr22	24179219	24182229	E072	30946
chr22	24108836	24111069	E073	-37204
chr22	24128387	24130388	E073	-17885
chr22	24179219	24182229	E073	30946
chr22	24108836	24111069	E074	-37204
chr22	24128387	24130388	E074	-17885
chr22	24179219	24182229	E074	30946
chr22	24128387	24130388	E081	-17885
chr22	24108836	24111069	E082	-37204
chr22	24128387	24130388	E082	-17885
chr22	24179219	24182229	E082	30946