rs17357905

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLFNL1 : Intron Variant
SLFNL1-AS1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0230 (6866/29838,GnomAD)
C=0198 (5793/29118,TOPMED)
C=0187 (938/5008,1000G)
C=0321 (1237/3854,ALSPAC)
C=0327 (1212/3708,TWINSUK)

Position: chr1:41018645 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 87 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.41018645T>C
GRCh37.p13 chr 1	NC_000001.10:g.41484317T>C

Gene: SLFNL1, schlafen like 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLFNL1 transcript variant 2	NM_001168247.2:c.	N/A	Intron Variant
SLFNL1 transcript variant 3	NM_001300859.1:c.	N/A	Intron Variant
SLFNL1 transcript variant 1	NM_144990.3:c.	N/A	Intron Variant
SLFNL1 transcript variant X1	XM_005270597.2:c.	N/A	Intron Variant
SLFNL1 transcript variant X7	XM_005270598.2:c.	N/A	Intron Variant
SLFNL1 transcript variant X8	XM_005270599.2:c.	N/A	Intron Variant
SLFNL1 transcript variant X7	XM_006710432.3:c.	N/A	Intron Variant
SLFNL1 transcript variant X2	XM_011540943.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X3	XM_011540945.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X3	XM_011540947.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X4	XM_011540948.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X6	XM_011540949.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X11	XM_011540950.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X6	XM_011540951.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X10	XM_011540952.2:c.	N/A	Intron Variant
SLFNL1 transcript variant X12	XM_011540953.2:c.	N/A	Intron Variant
SLFNL1 transcript variant X14	XM_011540954.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X15	XM_017000573.1:c.	N/A	Intron Variant
SLFNL1 transcript variant X16	XM_017000574.1:c.	N/A	Intron Variant

Gene: SLFNL1-AS1, SLFNL1 antisense RNA 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLFNL1-AS1 transcript	NR_037868.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.967	C=0.033
1000Genomes	American	Sub	694	T=0.700	C=0.300
1000Genomes	East Asian	Sub	1008	T=0.831	C=0.169
1000Genomes	Europe	Sub	1006	T=0.695	C=0.305
1000Genomes	Global	Study-wide	5008	T=0.813	C=0.187
1000Genomes	South Asian	Sub	978	T=0.780	C=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.679	C=0.321
The Genome Aggregation Database	African	Sub	8704	T=0.930	C=0.070
The Genome Aggregation Database	American	Sub	838	T=0.720	C=0.280
The Genome Aggregation Database	East Asian	Sub	1612	T=0.885	C=0.115
The Genome Aggregation Database	Europe	Sub	18382	T=0.687	C=0.312
The Genome Aggregation Database	Global	Study-wide	29838	T=0.769	C=0.230
The Genome Aggregation Database	Other	Sub	302	T=0.700	C=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.801	C=0.198
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.673	C=0.327

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
rs17357905	0.000485	alcohol dependence	21314694

eQTL of rs17357905 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:41484317	RP11-399E6.1	ENSG00000235358.1	T>C	6.4919e-3	-223728	Putamen_basal_ganglia

meQTL of rs17357905 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	41447103	41447170	E067	-37147
chr1	41450900	41451314	E067	-33003
chr1	41451687	41451768	E067	-32549
chr1	41467964	41468054	E067	-16263
chr1	41468143	41468220	E067	-16097
chr1	41468361	41468405	E067	-15912
chr1	41468660	41468747	E067	-15570
chr1	41468767	41468830	E067	-15487
chr1	41468859	41468974	E067	-15343
chr1	41469224	41469845	E067	-14472
chr1	41447103	41447170	E068	-37147
chr1	41447215	41447798	E068	-36519
chr1	41451687	41451768	E068	-32549
chr1	41467964	41468054	E068	-16263
chr1	41468143	41468220	E068	-16097
chr1	41468361	41468405	E068	-15912
chr1	41468660	41468747	E068	-15570
chr1	41468767	41468830	E068	-15487
chr1	41468859	41468974	E068	-15343
chr1	41469224	41469845	E068	-14472
chr1	41479612	41479840	E068	-4477
chr1	41479935	41479985	E068	-4332
chr1	41479989	41480043	E068	-4274
chr1	41447103	41447170	E069	-37147
chr1	41467964	41468054	E069	-16263
chr1	41468143	41468220	E069	-16097
chr1	41468361	41468405	E069	-15912
chr1	41468660	41468747	E069	-15570
chr1	41468767	41468830	E069	-15487
chr1	41468859	41468974	E069	-15343
chr1	41469224	41469845	E069	-14472
chr1	41511994	41512051	E069	27677
chr1	41438162	41438247	E071	-46070
chr1	41447103	41447170	E071	-37147
chr1	41448987	41449237	E071	-35080
chr1	41467964	41468054	E071	-16263
chr1	41468143	41468220	E071	-16097
chr1	41468361	41468405	E071	-15912
chr1	41468660	41468747	E071	-15570
chr1	41468767	41468830	E071	-15487
chr1	41468859	41468974	E071	-15343
chr1	41469224	41469845	E071	-14472
chr1	41437691	41437912	E072	-46405
chr1	41438162	41438247	E072	-46070
chr1	41447103	41447170	E072	-37147
chr1	41467964	41468054	E072	-16263
chr1	41468143	41468220	E072	-16097
chr1	41468361	41468405	E072	-15912
chr1	41468660	41468747	E072	-15570
chr1	41468767	41468830	E072	-15487
chr1	41468859	41468974	E072	-15343
chr1	41469224	41469845	E072	-14472
chr1	41447215	41447798	E073	-36519
chr1	41451687	41451768	E073	-32549
chr1	41452342	41452418	E073	-31899
chr1	41452614	41452977	E073	-31340
chr1	41452999	41453676	E073	-30641
chr1	41468361	41468405	E073	-15912
chr1	41468660	41468747	E073	-15570
chr1	41468767	41468830	E073	-15487
chr1	41468859	41468974	E073	-15343
chr1	41469224	41469845	E073	-14472
chr1	41479612	41479840	E073	-4477
chr1	41479935	41479985	E073	-4332
chr1	41479989	41480043	E073	-4274
chr1	41511994	41512051	E073	27677
chr1	41512104	41512649	E073	27787
chr1	41467964	41468054	E074	-16263
chr1	41468143	41468220	E074	-16097
chr1	41468361	41468405	E074	-15912
chr1	41468660	41468747	E074	-15570
chr1	41468767	41468830	E074	-15487
chr1	41468859	41468974	E074	-15343
chr1	41469224	41469845	E074	-14472
chr1	41511994	41512051	E074	27677
chr1	41447215	41447798	E081	-36519
chr1	41447895	41447996	E081	-36321
chr1	41450900	41451314	E081	-33003
chr1	41511399	41511832	E081	27082
chr1	41511994	41512051	E081	27677
chr1	41512104	41512649	E081	27787
chr1	41447103	41447170	E082	-37147
chr1	41447215	41447798	E082	-36519
chr1	41450900	41451314	E082	-33003
chr1	41511399	41511832	E082	27082
chr1	41511994	41512051	E082	27677
chr1	41512104	41512649	E082	27787

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	41444551	41447035	E067	-37282
chr1	41444551	41447035	E068	-37282
chr1	41444551	41447035	E069	-37282
chr1	41444551	41447035	E070	-37282
chr1	41444551	41447035	E071	-37282
chr1	41444551	41447035	E072	-37282
chr1	41444551	41447035	E073	-37282
chr1	41444551	41447035	E074	-37282
chr1	41444551	41447035	E081	-37282
chr1	41444551	41447035	E082	-37282