rs268487

Homo sapiens
A>G
SEMA5A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0447 (13396/29924,GnomAD)
A==0431 (12573/29118,TOPMED)
A==0425 (2126/5008,1000G)
A==0490 (1889/3854,ALSPAC)
A==0498 (1847/3708,TWINSUK)
chr5:9403862 (GRCh38.p7) (5p15.31)
AD
GWASdb2
1   publication(s)
See rs on genome
58 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.9403862A>G
GRCh37.p13 chr 5NC_000005.9:g.9403974A>G
SEMA5A RefSeqGeneNG_016410.1:g.147260T>C

Gene: SEMA5A, semaphorin 5A(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SEMA5A transcriptNM_003966.2:c.N/AIntron Variant
SEMA5A transcript variant X3XM_006714506.2:c.N/AIntron Variant
SEMA5A transcript variant X5XM_006714507.3:c.N/AIntron Variant
SEMA5A transcript variant X1XM_011514155.2:c.N/AIntron Variant
SEMA5A transcript variant X2XM_011514156.1:c.N/AIntron Variant
SEMA5A transcript variant X4XM_011514157.1:c.N/AIntron Variant
SEMA5A transcript variant X6XM_011514158.1:c.N/AIntron Variant
SEMA5A transcript variant X8XM_017010016.1:c.N/AIntron Variant
SEMA5A transcript variant X7XM_011514159.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.344G=0.656
1000GenomesAmericanSub694A=0.350G=0.650
1000GenomesEast AsianSub1008A=0.397G=0.603
1000GenomesEuropeSub1006A=0.520G=0.480
1000GenomesGlobalStudy-wide5008A=0.425G=0.575
1000GenomesSouth AsianSub978A=0.510G=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.490G=0.510
The Genome Aggregation DatabaseAfricanSub8700A=0.371G=0.629
The Genome Aggregation DatabaseAmericanSub836A=0.380G=0.620
The Genome Aggregation DatabaseEast AsianSub1614A=0.369G=0.631
The Genome Aggregation DatabaseEuropeSub18472A=0.493G=0.506
The Genome Aggregation DatabaseGlobalStudy-wide29924A=0.447G=0.552
The Genome Aggregation DatabaseOtherSub302A=0.440G=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.431G=0.568
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.498G=0.502
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
rs2684870.00085alcohol dependence20201924

eQTL of rs268487 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 rs268487 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 )
chr593564119356819E067-47155
chr593573809357778E067-46196
chr594299609430050E06725986
chr594300819430131E06726107
chr594316119432376E06727637
chr594522899452540E06748315
chr593564119356819E068-47155
chr593573809357778E068-46196
chr594304789430892E06826504
chr594314039431557E06827429
chr594316119432376E06827637
chr593564119356819E069-47155
chr594200619420235E06916087
chr594299609430050E06925986
chr594304789430892E06926504
chr594314039431557E06927429
chr594316119432376E06927637
chr594324419432544E06928467
chr594522899452540E06948315
chr593564119356819E070-47155
chr593573809357778E070-46196
chr593657219365942E070-38032
chr594316119432376E07027637
chr594460909446767E07042116
chr594498819449931E07045907
chr594500849450152E07046110
chr594522899452540E07048315
chr593546059354755E071-49219
chr593564119356819E071-47155
chr593573809357778E071-46196
chr593631799364214E071-39760
chr594304789430892E07126504
chr594314039431557E07127429
chr594316119432376E07127637
chr594324419432544E07128467
chr594460909446767E07142116
chr594522899452540E07148315
chr593564119356819E072-47155
chr594287429429246E07224768
chr594299609430050E07225986
chr594304789430892E07226504
chr594314039431557E07227429
chr594316119432376E07227637
chr594511779451539E07247203
chr594299609430050E07325986
chr594300819430131E07326107
chr594304789430892E07326504
chr594314039431557E07327429
chr593564119356819E074-47155
chr593573809357778E074-46196
chr594299609430050E07425986
chr594300819430131E07426107
chr594304789430892E07426504
chr594314039431557E07427429
chr594316119432376E07427637
chr594388739440959E07434899
chr594511779451539E07447203
chr594522899452540E07448315