rs17653439

Homo sapiens
G>A
C10orf88 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0042 (1284/29982,GnomAD)
A=0034 (1011/29118,TOPMED)
A=0020 (99/5008,1000G)
A=0076 (292/3854,ALSPAC)
A=0081 (300/3708,TWINSUK)
chr10:122930775 (GRCh38.p7) (10q26.13)
AD
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.122930775G>A
GRCh37.p13 chr 10NC_000010.10:g.124690291G>A

Gene: C10orf88, chromosome 10 open reading frame 88(minus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
C10orf88 transcriptNM_024942.3:c.N/ADownstream Transcript Variant
C10orf88 transcript variant X1XR_001747204.1:n.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.998A=0.002
1000GenomesAmericanSub694G=0.990A=0.010
1000GenomesEast AsianSub1008G=0.999A=0.001
1000GenomesEuropeSub1006G=0.946A=0.054
1000GenomesGlobalStudy-wide5008G=0.980A=0.020
1000GenomesSouth AsianSub978G=0.960A=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.924A=0.076
The Genome Aggregation DatabaseAfricanSub8728G=0.989A=0.011
The Genome Aggregation DatabaseAmericanSub838G=0.970A=0.030
The Genome Aggregation DatabaseEast AsianSub1622G=0.999A=0.001
The Genome Aggregation DatabaseEuropeSub18492G=0.937A=0.062
The Genome Aggregation DatabaseGlobalStudy-wide29982G=0.957A=0.042
The Genome Aggregation DatabaseOtherSub302G=0.980A=0.020
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.965A=0.034
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.919A=0.081
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
rs176534390.00075alcohol dependence20201924
rs176534390.00089alcohol dependence20201924

eQTL of rs17653439 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 rs17653439 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 )
chr10124712308124712362E06722017
chr10124712499124712580E06722208
chr10124640368124640417E068-49874
chr10124738902124739109E06848611
chr10124711363124711413E06921072
chr10124712308124712362E06922017
chr10124712499124712580E06922208
chr10124712308124712362E07122017
chr10124712499124712580E07122208
chr10124712499124712580E07222208
chr10124738902124739109E07248611
chr10124712499124712580E07422208
chr10124711363124711413E08121072
chr10124712308124712362E08122017
chr10124712499124712580E08122208
chr10124712499124712580E08222208
chr10124715091124715141E08224800
chr10124733273124733628E08242982
chr10124733682124733800E08243391








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr10124712887124713324E06722596
chr10124713393124714474E06723102
chr10124712887124713324E06822596
chr10124713393124714474E06823102
chr10124714645124714688E06824354
chr10124712887124713324E06922596
chr10124713393124714474E06923102
chr10124714645124714688E06924354
chr10124712887124713324E07022596
chr10124713393124714474E07023102
chr10124712887124713324E07122596
chr10124713393124714474E07123102
chr10124712887124713324E07222596
chr10124713393124714474E07223102
chr10124712887124713324E07322596
chr10124713393124714474E07323102
chr10124712887124713324E07422596
chr10124713393124714474E07423102
chr10124712887124713324E08122596
chr10124712887124713324E08222596
chr10124713393124714474E08223102