rs7717860

Homo sapiens
C>A
C5orf24 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0153 (4598/29956,GnomAD)
A=0159 (4652/29118,TOPMED)
A=0218 (1090/5008,1000G)
A=0154 (595/3854,ALSPAC)
A=0155 (576/3708,TWINSUK)
chr5:134854535 (GRCh38.p7) (5q31.1)
AD
GWASdb2
1   publication(s)
See rs on genome
44 Enhancers around
30 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.134854535C>A
GRCh37.p13 chr 5NC_000005.9:g.134190225C>A

Gene: C5orf24, chromosome 5 open reading frame 24(plus strand)

Molecule type Change Amino acid[Codon] SO Term
C5orf24 transcript variant 1NM_001135586.1:c.N/AIntron Variant
C5orf24 transcript variant 3NM_001300894.1:c.N/AIntron Variant
C5orf24 transcript variant 2NM_152409.3:c.N/AIntron Variant
C5orf24 transcript variant X1XM_005271889.3:c.N/AIntron Variant
C5orf24 transcript variant X2XM_017009049.1:c.N/AIntron Variant
C5orf24 transcript variant X3XM_017009050.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.837A=0.163
1000GenomesAmericanSub694C=0.900A=0.100
1000GenomesEast AsianSub1008C=0.672A=0.328
1000GenomesEuropeSub1006C=0.874A=0.126
1000GenomesGlobalStudy-wide5008C=0.782A=0.218
1000GenomesSouth AsianSub978C=0.640A=0.360
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.846A=0.154
The Genome Aggregation DatabaseAfricanSub8716C=0.836A=0.164
The Genome Aggregation DatabaseAmericanSub838C=0.910A=0.090
The Genome Aggregation DatabaseEast AsianSub1612C=0.610A=0.390
The Genome Aggregation DatabaseEuropeSub18488C=0.868A=0.131
The Genome Aggregation DatabaseGlobalStudy-wide29956C=0.846A=0.153
The Genome Aggregation DatabaseOtherSub302C=0.860A=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.840A=0.159
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.845A=0.155
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs77178609.7E-05alcoholism (heaviness of drinking)21529783

eQTL of rs7717860 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 rs7717860 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 )
chr5134211994134212232E06721769
chr5134213042134213098E06722817
chr5134213136134213262E06722911
chr5134214177134214349E06723952
chr5134184843134185327E068-4898
chr5134186417134186567E068-3658
chr5134186836134187044E068-3181
chr5134187069134187394E068-2831
chr5134211994134212232E06821769
chr5134213042134213098E06822817
chr5134213136134213262E06822911
chr5134193424134193478E0693199
chr5134193483134193558E0693258
chr5134208894134209071E06918669
chr5134211994134212232E06921769
chr5134215896134215987E06925671
chr5134186836134187044E070-3181
chr5134187069134187394E070-2831
chr5134193424134193478E0713199
chr5134193483134193558E0713258
chr5134208894134209071E07118669
chr5134213042134213098E07122817
chr5134215896134215987E07125671
chr5134184843134185327E072-4898
chr5134193424134193478E0723199
chr5134193483134193558E0723258
chr5134208894134209071E07218669
chr5134213042134213098E07222817
chr5134213136134213262E07222911
chr5134214177134214349E07223952
chr5134211798134211888E07321573
chr5134211994134212232E07321769
chr5134213042134213098E07322817
chr5134213136134213262E07322911
chr5134193424134193478E0743199
chr5134193483134193558E0743258
chr5134211994134212232E07421769
chr5134214177134214349E07423952
chr5134183932134183987E081-6238
chr5134211798134211888E08121573
chr5134211994134212232E08121769
chr5134213042134213098E08222817
chr5134213136134213262E08222911
chr5134214177134214349E08223952










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5134180822134182715E067-7510
chr5134182717134182883E067-7342
chr5134209265134211316E06719040
chr5134180822134182715E068-7510
chr5134182717134182883E068-7342
chr5134209265134211316E06819040
chr5134180822134182715E069-7510
chr5134182717134182883E069-7342
chr5134209265134211316E06919040
chr5134180822134182715E070-7510
chr5134182717134182883E070-7342
chr5134209265134211316E07019040
chr5134180822134182715E071-7510
chr5134182717134182883E071-7342
chr5134209265134211316E07119040
chr5134180822134182715E072-7510
chr5134182717134182883E072-7342
chr5134209265134211316E07219040
chr5134180822134182715E073-7510
chr5134182717134182883E073-7342
chr5134209265134211316E07319040
chr5134180822134182715E074-7510
chr5134182717134182883E074-7342
chr5134209265134211316E07419040
chr5134180822134182715E081-7510
chr5134182717134182883E081-7342
chr5134209265134211316E08119040
chr5134180822134182715E082-7510
chr5134182717134182883E082-7342
chr5134209265134211316E08219040