rs17358933

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC440600 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0164 (4917/29946,GnomAD)
A=0149 (4356/29118,TOPMED)
A=0193 (966/5008,1000G)
A=0180 (695/3854,ALSPAC)
A=0178 (659/3708,TWINSUK)

Position: chr1:110306583 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 134 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.110306583G>A
GRCh37.p13 chr 1	NC_000001.10:g.110849205G>A

Gene: LOC440600, uncharacterized LOC440600(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RBM15-AS1 transcript	NR_036595.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.880	A=0.120
1000Genomes	American	Sub	694	G=0.830	A=0.170
1000Genomes	East Asian	Sub	1008	G=0.741	A=0.259
1000Genomes	Europe	Sub	1006	G=0.827	A=0.173
1000Genomes	Global	Study-wide	5008	G=0.807	A=0.193
1000Genomes	South Asian	Sub	978	G=0.740	A=0.260
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.820	A=0.180
The Genome Aggregation Database	African	Sub	8722	G=0.880	A=0.120
The Genome Aggregation Database	American	Sub	838	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1622	G=0.729	A=0.271
The Genome Aggregation Database	Europe	Sub	18462	G=0.826	A=0.173
The Genome Aggregation Database	Global	Study-wide	29946	G=0.835	A=0.164
The Genome Aggregation Database	Other	Sub	302	G=0.750	A=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.850	A=0.149
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.822	A=0.178

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

P-Value

SNP ID	p-value	Traits	Study
rs17358933	0.000837	alcohol dependence	21314694

eQTL of rs17358933 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:110849205	RP5-1074L1.1	ENSG00000227963.1	G>A	2.4997e-16	-12299	Cerebellum
Chr1:110849205	RP5-1074L1.1	ENSG00000227963.1	G>A	6.7681e-3	-12299	Brain_Spinal_cord_cervical

meQTL of rs17358933 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	110855128	110855827	E067	5923
chr1	110883569	110883637	E067	34364
chr1	110883982	110884065	E067	34777
chr1	110884125	110884175	E067	34920
chr1	110886317	110886556	E067	37112
chr1	110889329	110889462	E067	40124
chr1	110889492	110889602	E067	40287
chr1	110889973	110890029	E067	40768
chr1	110890146	110890274	E067	40941
chr1	110890284	110890334	E067	41079
chr1	110890377	110890451	E067	41172
chr1	110890783	110890838	E067	41578
chr1	110891400	110891672	E067	42195
chr1	110891953	110892030	E067	42748
chr1	110893147	110893353	E067	43942
chr1	110893436	110893527	E067	44231
chr1	110855128	110855827	E068	5923
chr1	110883982	110884065	E068	34777
chr1	110884125	110884175	E068	34920
chr1	110884286	110884336	E068	35081
chr1	110886317	110886556	E068	37112
chr1	110887192	110887372	E068	37987
chr1	110889492	110889602	E068	40287
chr1	110889973	110890029	E068	40768
chr1	110890146	110890274	E068	40941
chr1	110890284	110890334	E068	41079
chr1	110890377	110890451	E068	41172
chr1	110890783	110890838	E068	41578
chr1	110891400	110891672	E068	42195
chr1	110891953	110892030	E068	42748
chr1	110799323	110799375	E069	-49830
chr1	110883569	110883637	E069	34364
chr1	110884648	110884767	E069	35443
chr1	110884875	110884976	E069	35670
chr1	110889329	110889462	E069	40124
chr1	110889492	110889602	E069	40287
chr1	110889973	110890029	E069	40768
chr1	110890146	110890274	E069	40941
chr1	110890284	110890334	E069	41079
chr1	110890377	110890451	E069	41172
chr1	110890783	110890838	E069	41578
chr1	110891400	110891672	E069	42195
chr1	110891953	110892030	E069	42748
chr1	110801524	110801621	E070	-47584
chr1	110843141	110843412	E070	-5793
chr1	110889492	110889602	E070	40287
chr1	110889973	110890029	E070	40768
chr1	110890783	110890838	E070	41578
chr1	110891400	110891672	E070	42195
chr1	110893147	110893353	E070	43942
chr1	110893436	110893527	E070	44231
chr1	110883982	110884065	E071	34777
chr1	110884125	110884175	E071	34920
chr1	110884286	110884336	E071	35081
chr1	110884498	110884635	E071	35293
chr1	110884648	110884767	E071	35443
chr1	110884875	110884976	E071	35670
chr1	110886317	110886556	E071	37112
chr1	110889329	110889462	E071	40124
chr1	110889492	110889602	E071	40287
chr1	110889973	110890029	E071	40768
chr1	110890146	110890274	E071	40941
chr1	110890284	110890334	E071	41079
chr1	110890377	110890451	E071	41172
chr1	110890783	110890838	E071	41578
chr1	110891953	110892030	E071	42748
chr1	110852427	110852750	E072	3222
chr1	110852860	110853026	E072	3655
chr1	110853043	110853290	E072	3838
chr1	110853909	110853975	E072	4704
chr1	110883569	110883637	E072	34364
chr1	110883982	110884065	E072	34777
chr1	110884125	110884175	E072	34920
chr1	110884498	110884635	E072	35293
chr1	110884648	110884767	E072	35443
chr1	110884875	110884976	E072	35670
chr1	110886317	110886556	E072	37112
chr1	110890146	110890274	E072	40941
chr1	110890284	110890334	E072	41079
chr1	110890377	110890451	E072	41172
chr1	110890783	110890838	E072	41578
chr1	110852427	110852750	E073	3222
chr1	110852860	110853026	E073	3655
chr1	110853043	110853290	E073	3838
chr1	110855128	110855827	E073	5923
chr1	110884286	110884336	E073	35081
chr1	110884498	110884635	E073	35293
chr1	110884648	110884767	E073	35443
chr1	110884875	110884976	E073	35670
chr1	110886317	110886556	E073	37112
chr1	110883569	110883637	E074	34364
chr1	110883982	110884065	E074	34777
chr1	110884125	110884175	E074	34920
chr1	110884286	110884336	E074	35081
chr1	110884498	110884635	E074	35293
chr1	110884648	110884767	E074	35443
chr1	110886317	110886556	E074	37112
chr1	110887192	110887372	E074	37987
chr1	110889329	110889462	E074	40124
chr1	110889492	110889602	E074	40287
chr1	110889973	110890029	E074	40768
chr1	110890146	110890274	E074	40941
chr1	110890284	110890334	E074	41079
chr1	110890377	110890451	E074	41172
chr1	110890783	110890838	E074	41578
chr1	110891400	110891672	E074	42195
chr1	110809640	110809712	E081	-39493
chr1	110849910	110849960	E081	705
chr1	110850359	110850449	E081	1154
chr1	110883569	110883637	E081	34364
chr1	110883982	110884065	E081	34777
chr1	110884125	110884175	E081	34920
chr1	110884286	110884336	E081	35081
chr1	110884498	110884635	E081	35293
chr1	110884648	110884767	E081	35443
chr1	110884875	110884976	E081	35670
chr1	110886317	110886556	E081	37112
chr1	110889492	110889602	E081	40287
chr1	110889973	110890029	E081	40768
chr1	110890146	110890274	E081	40941
chr1	110890284	110890334	E081	41079
chr1	110890377	110890451	E081	41172
chr1	110890783	110890838	E081	41578
chr1	110891400	110891672	E081	42195
chr1	110850359	110850449	E082	1154
chr1	110850564	110850676	E082	1359
chr1	110889329	110889462	E082	40124
chr1	110889492	110889602	E082	40287
chr1	110889973	110890029	E082	40768
chr1	110890146	110890274	E082	40941
chr1	110890783	110890838	E082	41578
chr1	110891400	110891672	E082	42195
chr1	110893147	110893353	E082	43942
chr1	110893436	110893527	E082	44231

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	110880260	110883240	E067	31055
chr1	110880260	110883240	E068	31055
chr1	110880260	110883240	E069	31055
chr1	110880260	110883240	E070	31055
chr1	110880260	110883240	E071	31055
chr1	110880260	110883240	E072	31055
chr1	110880260	110883240	E073	31055
chr1	110880260	110883240	E074	31055
chr1	110880260	110883240	E082	31055