rs2833487

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SCAF4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0081 (2426/29928,GnomAD)
G=0091 (2677/29118,TOPMED)
G=0056 (282/5008,1000G)
G=0045 (172/3854,ALSPAC)
G=0042 (156/3708,TWINSUK)

Position: chr21:31715550 (GRCh38.p7) (21q22.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 102 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 21	NC_000021.9:g.31715550A>G
GRCh37.p13 chr 21	NC_000021.8:g.33087863A>G

Gene: SCAF4, SR-related CTD associated factor 4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCAF4 transcript variant 2	NM_001145444.1:c.	N/A	Intron Variant
SCAF4 transcript variant 3	NM_001145445.1:c.	N/A	Intron Variant
SCAF4 transcript variant 1	NM_020706.2:c.	N/A	Intron Variant
SCAF4 transcript variant X5	XM_005261017.2:c.	N/A	Intron Variant
SCAF4 transcript variant X2	XM_006724035.2:c.	N/A	Intron Variant
SCAF4 transcript variant X4	XM_006724036.2:c.	N/A	Intron Variant
SCAF4 transcript variant X1	XM_017028415.1:c.	N/A	Intron Variant
SCAF4 transcript variant X3	XM_017028416.1:c.	N/A	Intron Variant
SCAF4 transcript variant X6	XM_017028417.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.850	G=0.150
1000Genomes	American	Sub	694	A=0.980	G=0.020
1000Genomes	East Asian	Sub	1008	A=0.996	G=0.004
1000Genomes	Europe	Sub	1006	A=0.943	G=0.057
1000Genomes	Global	Study-wide	5008	A=0.944	G=0.056
1000Genomes	South Asian	Sub	978	A=0.990	G=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.955	G=0.045
The Genome Aggregation Database	African	Sub	8706	A=0.851	G=0.149
The Genome Aggregation Database	American	Sub	836	A=0.980	G=0.020
The Genome Aggregation Database	East Asian	Sub	1612	A=0.997	G=0.003
The Genome Aggregation Database	Europe	Sub	18472	A=0.940	G=0.060
The Genome Aggregation Database	Global	Study-wide	29928	A=0.918	G=0.081
The Genome Aggregation Database	Other	Sub	302	A=0.980	G=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.908	G=0.091
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.958	G=0.042

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs2833487	0.000604	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr21	33038215	33038309	E067	-49554
chr21	33038553	33038626	E067	-49237
chr21	33038752	33038825	E067	-49038
chr21	33038906	33039020	E067	-48843
chr21	33039086	33039231	E067	-48632
chr21	33039356	33039423	E067	-48440
chr21	33039450	33039574	E067	-48289
chr21	33082809	33082920	E067	-4943
chr21	33082939	33083253	E067	-4610
chr21	33086993	33087220	E067	-643
chr21	33087368	33087540	E067	-323
chr21	33101117	33101179	E067	13254
chr21	33101198	33101335	E067	13335
chr21	33101348	33101554	E067	13485
chr21	33101563	33101617	E067	13700
chr21	33101672	33101863	E067	13809
chr21	33038215	33038309	E068	-49554
chr21	33078743	33078864	E068	-8999
chr21	33078969	33079230	E068	-8633
chr21	33082939	33083253	E068	-4610
chr21	33083307	33083431	E068	-4432
chr21	33086733	33086957	E068	-906
chr21	33086993	33087220	E068	-643
chr21	33087368	33087540	E068	-323
chr21	33101117	33101179	E068	13254
chr21	33101198	33101335	E068	13335
chr21	33101348	33101554	E068	13485
chr21	33101563	33101617	E068	13700
chr21	33101672	33101863	E068	13809
chr21	33085708	33085758	E069	-2105
chr21	33086315	33086427	E069	-1436
chr21	33086476	33086570	E069	-1293
chr21	33086584	33086664	E069	-1199
chr21	33086733	33086957	E069	-906
chr21	33088698	33088768	E069	835
chr21	33101198	33101335	E069	13335
chr21	33101348	33101554	E069	13485
chr21	33101563	33101617	E069	13700
chr21	33101672	33101863	E069	13809
chr21	33085708	33085758	E070	-2105
chr21	33085826	33085902	E070	-1961
chr21	33086315	33086427	E070	-1436
chr21	33101198	33101335	E070	13335
chr21	33101348	33101554	E070	13485
chr21	33101563	33101617	E070	13700
chr21	33101672	33101863	E070	13809
chr21	33038215	33038309	E071	-49554
chr21	33038553	33038626	E071	-49237
chr21	33038752	33038825	E071	-49038
chr21	33038906	33039020	E071	-48843
chr21	33039086	33039231	E071	-48632
chr21	33082809	33082920	E071	-4943
chr21	33082939	33083253	E071	-4610
chr21	33083307	33083431	E071	-4432
chr21	33086584	33086664	E071	-1199
chr21	33086733	33086957	E071	-906
chr21	33086993	33087220	E071	-643
chr21	33087368	33087540	E071	-323
chr21	33095775	33095825	E071	7912
chr21	33096887	33096937	E071	9024
chr21	33097743	33097793	E071	9880
chr21	33097891	33097977	E071	10028
chr21	33101117	33101179	E071	13254
chr21	33101198	33101335	E071	13335
chr21	33101348	33101554	E071	13485
chr21	33101563	33101617	E071	13700
chr21	33101672	33101863	E071	13809
chr21	33038215	33038309	E072	-49554
chr21	33038553	33038626	E072	-49237
chr21	33097743	33097793	E072	9880
chr21	33097891	33097977	E072	10028
chr21	33101117	33101179	E072	13254
chr21	33101198	33101335	E072	13335
chr21	33101348	33101554	E072	13485
chr21	33101563	33101617	E072	13700
chr21	33101672	33101863	E072	13809
chr21	33101348	33101554	E073	13485
chr21	33101563	33101617	E073	13700
chr21	33101672	33101863	E073	13809
chr21	33078743	33078864	E074	-8999
chr21	33078969	33079230	E074	-8633
chr21	33086584	33086664	E074	-1199
chr21	33086733	33086957	E074	-906
chr21	33086993	33087220	E074	-643
chr21	33087368	33087540	E074	-323
chr21	33100735	33100790	E074	12872
chr21	33101117	33101179	E074	13254
chr21	33101198	33101335	E074	13335
chr21	33101348	33101554	E074	13485
chr21	33101563	33101617	E074	13700
chr21	33101672	33101863	E074	13809
chr21	33101348	33101554	E081	13485
chr21	33101563	33101617	E081	13700
chr21	33101672	33101863	E081	13809
chr21	33128804	33128876	E081	40941
chr21	33130889	33130939	E081	43026
chr21	33083307	33083431	E082	-4432
chr21	33100365	33100472	E082	12502
chr21	33100549	33100589	E082	12686
chr21	33100735	33100790	E082	12872
chr21	33101117	33101179	E082	13254
chr21	33101198	33101335	E082	13335

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr21	33102731	33106445	E067	14868
chr21	33102731	33106445	E068	14868
chr21	33102731	33106445	E069	14868
chr21	33102731	33106445	E070	14868
chr21	33102731	33106445	E071	14868
chr21	33102731	33106445	E072	14868
chr21	33102731	33106445	E073	14868
chr21	33102731	33106445	E074	14868
chr21	33102731	33106445	E081	14868
chr21	33102731	33106445	E082	14868

rs2833487

Genomic Coordinates

Gene: SCAF4, SR-related CTD associated factor 4(minus strand)

Population Frequency

P-Value

eQTL of rs2833487 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2833487 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)