rs899940

Homo sapiens
T>G
SLFN5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0405 (12119/29888,GnomAD)
T==0388 (11316/29118,TOPMED)
T==0437 (2186/5008,1000G)
T==0372 (1435/3854,ALSPAC)
T==0372 (1378/3708,TWINSUK)
chr17:35259821 (GRCh38.p7) (17q12)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.35259821T>G
GRCh37.p13 chr 17NC_000017.10:g.33586840T>G

Gene: SLFN5, schlafen family member 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLFN5 transcript variant 1NM_144975.3:c.N/AIntron Variant
SLFN5 transcript variant X1XM_005257934.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.408G=0.592
1000GenomesAmericanSub694T=0.410G=0.590
1000GenomesEast AsianSub1008T=0.582G=0.418
1000GenomesEuropeSub1006T=0.371G=0.629
1000GenomesGlobalStudy-wide5008T=0.437G=0.563
1000GenomesSouth AsianSub978T=0.410G=0.590
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.372G=0.628
The Genome Aggregation DatabaseAfricanSub8694T=0.389G=0.611
The Genome Aggregation DatabaseAmericanSub834T=0.460G=0.540
The Genome Aggregation DatabaseEast AsianSub1612T=0.562G=0.438
The Genome Aggregation DatabaseEuropeSub18446T=0.398G=0.601
The Genome Aggregation DatabaseGlobalStudy-wide29888T=0.405G=0.594
The Genome Aggregation DatabaseOtherSub302T=0.310G=0.690
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.388G=0.611
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.372G=0.628
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs8999400.00086alcohol dependence20201924

eQTL of rs899940 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 rs899940 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 )
chr173358360233583988E069-2852
chr173357961533579659E071-7181
chr173357972433580014E071-6826
chr173358026433580325E071-6515
chr173358050133580567E071-6273
chr173358076933580905E071-5935
chr173358094733581012E071-5828
chr173358112333581177E071-5663
chr173358119733581779E071-5061
chr173358227833582318E071-4522
chr173358233533582402E071-4438
chr173358246733582651E071-4189
chr173358412433584705E071-2135
chr173359122433591264E0714384
chr173359193033591996E0715090
chr173359204433592112E0715204
chr173359228433592642E0715444
chr173359265433593107E0715814
chr173359327133593339E0716431
chr173359337333593423E0716533
chr173358233533582402E081-4438
chr173358246733582651E081-4189



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr173356882133572764E067-14076
chr173356882133572764E068-14076
chr173356882133572764E069-14076
chr173356882133572764E071-14076
chr173356882133572764E072-14076
chr173356882133572764E073-14076
chr173356882133572764E074-14076
chr173356882133572764E082-14076