rs1033190

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

IGSF21 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0188 (5644/29944,GnomAD)
T=0176 (5151/29118,TOPMED)
T=0166 (833/5008,1000G)
T=0180 (692/3854,ALSPAC)
T=0197 (732/3708,TWINSUK)

Position: chr1:18202354 (GRCh38.p7) (1p36.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.18202354G>T
GRCh37.p13 chr 1	NC_000001.10:g.18528848G>T
IGSF21 RefSeqGene	NG_027535.1:g.99609G>T

Gene: IGSF21, immunoglobin superfamily member 21(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IGSF21 transcript	NM_032880.4:c.	N/A	Intron Variant
IGSF21 transcript variant X3	XM_011542319.2:c.	N/A	Intron Variant
IGSF21 transcript variant X1	XM_017002604.1:c.	N/A	Genic Upstream Transcript Variant
IGSF21 transcript variant X3	XM_017002605.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.838	T=0.162
1000Genomes	American	Sub	694	G=0.830	T=0.170
1000Genomes	East Asian	Sub	1008	G=0.878	T=0.122
1000Genomes	Europe	Sub	1006	G=0.786	T=0.214
1000Genomes	Global	Study-wide	5008	G=0.834	T=0.166
1000Genomes	South Asian	Sub	978	G=0.830	T=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.820	T=0.180
The Genome Aggregation Database	African	Sub	8716	G=0.852	T=0.148
The Genome Aggregation Database	American	Sub	838	G=0.870	T=0.130
The Genome Aggregation Database	East Asian	Sub	1618	G=0.875	T=0.125
The Genome Aggregation Database	Europe	Sub	18472	G=0.785	T=0.214
The Genome Aggregation Database	Global	Study-wide	29944	G=0.811	T=0.188
The Genome Aggregation Database	Other	Sub	300	G=0.690	T=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.823	T=0.176
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.803	T=0.197

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
rs1033190	0.000615	alcohol dependence	20201924

eQTL of rs1033190 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 rs1033190 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	18517888	18518382	E067	-10466
chr1	18518512	18518650	E067	-10198
chr1	18556211	18556511	E067	27363
chr1	18556842	18557058	E067	27994
chr1	18557261	18557311	E067	28413
chr1	18557355	18557679	E067	28507
chr1	18556842	18557058	E068	27994
chr1	18557261	18557311	E068	28413
chr1	18557355	18557679	E068	28507
chr1	18502575	18502919	E069	-25929
chr1	18503109	18503351	E069	-25497
chr1	18517888	18518382	E069	-10466
chr1	18518512	18518650	E069	-10198
chr1	18525881	18525931	E069	-2917
chr1	18526699	18526853	E069	-1995
chr1	18556211	18556511	E069	27363
chr1	18556842	18557058	E069	27994
chr1	18557261	18557311	E069	28413
chr1	18557355	18557679	E069	28507
chr1	18502437	18502503	E070	-26345
chr1	18502575	18502919	E070	-25929
chr1	18517888	18518382	E070	-10466
chr1	18518512	18518650	E070	-10198
chr1	18526021	18526621	E070	-2227
chr1	18556211	18556511	E070	27363
chr1	18556842	18557058	E070	27994
chr1	18557261	18557311	E070	28413
chr1	18557355	18557679	E070	28507
chr1	18497844	18497953	E071	-30895
chr1	18498271	18498368	E071	-30480
chr1	18517888	18518382	E071	-10466
chr1	18538322	18538585	E071	9474
chr1	18551703	18552127	E071	22855
chr1	18556842	18557058	E071	27994
chr1	18517210	18517474	E072	-11374
chr1	18517888	18518382	E072	-10466
chr1	18536743	18536996	E072	7895
chr1	18537089	18537143	E072	8241
chr1	18538322	18538585	E072	9474
chr1	18556842	18557058	E072	27994
chr1	18557261	18557311	E072	28413
chr1	18557355	18557679	E072	28507
chr1	18576119	18576208	E072	47271
chr1	18502437	18502503	E073	-26345
chr1	18526021	18526621	E073	-2227
chr1	18526699	18526853	E073	-1995
chr1	18531136	18531338	E073	2288
chr1	18538322	18538585	E073	9474
chr1	18555709	18555863	E073	26861
chr1	18556211	18556511	E073	27363
chr1	18556842	18557058	E073	27994
chr1	18557261	18557311	E073	28413
chr1	18557355	18557679	E073	28507
chr1	18576119	18576208	E073	47271
chr1	18576243	18576516	E073	47395
chr1	18481150	18481210	E074	-47638
chr1	18481329	18481512	E074	-47336
chr1	18488116	18488227	E074	-40621
chr1	18517888	18518382	E074	-10466
chr1	18556211	18556511	E074	27363
chr1	18556842	18557058	E074	27994
chr1	18557261	18557311	E074	28413
chr1	18557355	18557679	E074	28507
chr1	18500562	18501005	E081	-27843
chr1	18501877	18501942	E081	-26906
chr1	18513510	18513802	E081	-15046
chr1	18516500	18516550	E081	-12298
chr1	18517210	18517474	E081	-11374
chr1	18517888	18518382	E081	-10466
chr1	18518512	18518650	E081	-10198
chr1	18519426	18519507	E081	-9341
chr1	18524446	18524526	E081	-4322
chr1	18524842	18525159	E081	-3689
chr1	18525881	18525931	E081	-2917
chr1	18526021	18526621	E081	-2227
chr1	18526699	18526853	E081	-1995
chr1	18536743	18536996	E081	7895
chr1	18537089	18537143	E081	8241
chr1	18538322	18538585	E081	9474
chr1	18551703	18552127	E081	22855
chr1	18554815	18554909	E081	25967
chr1	18555259	18555340	E081	26411
chr1	18555709	18555863	E081	26861
chr1	18556211	18556511	E081	27363
chr1	18556842	18557058	E081	27994
chr1	18557261	18557311	E081	28413
chr1	18557355	18557679	E081	28507
chr1	18564823	18564901	E081	35975
chr1	18565254	18565347	E081	36406
chr1	18565592	18565723	E081	36744
chr1	18565976	18566486	E081	37128
chr1	18568467	18568746	E081	39619
chr1	18570269	18570365	E081	41421
chr1	18570461	18570681	E081	41613
chr1	18576119	18576208	E081	47271
chr1	18576243	18576516	E081	47395
chr1	18576545	18576595	E081	47697
chr1	18576665	18576784	E081	47817
chr1	18516500	18516550	E082	-12298
chr1	18517210	18517474	E082	-11374
chr1	18518512	18518650	E082	-10198
chr1	18519426	18519507	E082	-9341
chr1	18524000	18524060	E082	-4788
chr1	18524113	18524165	E082	-4683
chr1	18524446	18524526	E082	-4322
chr1	18524842	18525159	E082	-3689
chr1	18525881	18525931	E082	-2917
chr1	18526021	18526621	E082	-2227
chr1	18526699	18526853	E082	-1995
chr1	18536743	18536996	E082	7895
chr1	18551703	18552127	E082	22855
chr1	18554815	18554909	E082	25967
chr1	18555259	18555340	E082	26411
chr1	18555709	18555863	E082	26861
chr1	18556211	18556511	E082	27363
chr1	18556842	18557058	E082	27994
chr1	18557261	18557311	E082	28413
chr1	18557355	18557679	E082	28507
chr1	18565976	18566486	E082	37128