rs2471503

Homo sapiens
T>C
CEP290 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0480 (14374/29888,GnomAD)
C=0448 (13048/29118,TOPMED)
T==0478 (2395/5008,1000G)
T==0386 (1488/3854,ALSPAC)
T==0383 (1421/3708,TWINSUK)
chr12:88069674 (GRCh38.p7) (12q21.32)
AD
GWASdb2
1   publication(s)
See rs on genome
46 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.88069674T>C
GRCh37.p13 chr 12NC_000012.11:g.88463451T>C
CEP290 RefSeqGeneNG_008417.1:g.77543A>G

Gene: CEP290, centrosomal protein 290(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CEP290 transcriptNM_025114.3:c.N/AIntron Variant
CEP290 transcript variant X1XM_011538756.2:c.N/AIntron Variant
CEP290 transcript variant X2XM_011538757.2:c.N/AIntron Variant
CEP290 transcript variant X3XM_011538758.2:c.N/AIntron Variant
CEP290 transcript variant X4XM_011538759.2:c.N/AIntron Variant
CEP290 transcript variant X5XM_011538760.1:c.N/AIntron Variant
CEP290 transcript variant X7XM_011538761.1:c.N/AIntron Variant
CEP290 transcript variant X12XM_011538762.2:c.N/AIntron Variant
CEP290 transcript variant X13XM_011538763.2:c.N/AIntron Variant
CEP290 transcript variant X15XM_011538764.2:c.N/AIntron Variant
CEP290 transcript variant X16XM_011538765.2:c.N/AIntron Variant
CEP290 transcript variant X17XM_011538766.2:c.N/AIntron Variant
CEP290 transcript variant X6XM_017019980.1:c.N/AIntron Variant
CEP290 transcript variant X8XM_017019981.1:c.N/AIntron Variant
CEP290 transcript variant X9XM_017019982.1:c.N/AIntron Variant
CEP290 transcript variant X14XM_017019983.1:c.N/AIntron Variant
CEP290 transcript variant X10XR_001748869.1:n.N/AIntron Variant
CEP290 transcript variant X11XR_001748870.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.845C=0.155
1000GenomesAmericanSub694T=0.410C=0.590
1000GenomesEast AsianSub1008T=0.268C=0.732
1000GenomesEuropeSub1006T=0.363C=0.637
1000GenomesGlobalStudy-wide5008T=0.478C=0.522
1000GenomesSouth AsianSub978T=0.370C=0.630
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.386C=0.614
The Genome Aggregation DatabaseAfricanSub8712T=0.755C=0.245
The Genome Aggregation DatabaseAmericanSub834T=0.400C=0.600
The Genome Aggregation DatabaseEast AsianSub1616T=0.227C=0.773
The Genome Aggregation DatabaseEuropeSub18424T=0.379C=0.620
The Genome Aggregation DatabaseGlobalStudy-wide29888T=0.480C=0.519
The Genome Aggregation DatabaseOtherSub302T=0.330C=0.670
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.551C=0.448
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.383C=0.617
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs24715030.000705alcohol dependence21314694

eQTL of rs2471503 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 rs2471503 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 )
chr128843582588436088E067-27363
chr128843331488433354E068-30097
chr128843582588436088E068-27363
chr128843615588436235E068-27216
chr128843085588430978E069-32473
chr128843109188431135E069-32316
chr128843118388431252E069-32199
chr128843125488431334E069-32117
chr128843154688431586E069-31865
chr128843185388431925E069-31526
chr128843194488432046E069-31405
chr128843206788432111E069-31340
chr128843213288432287E069-31164
chr128843582588436088E069-27363
chr128843615588436235E069-27216
chr128844706988447119E069-16332
chr128844714688447200E069-16251
chr128843085588430978E070-32473
chr128843109188431135E070-32316
chr128843118388431252E070-32199
chr128843125488431334E070-32117
chr128843085588430978E071-32473
chr128843582588436088E071-27363
chr128843615588436235E071-27216
chr128843556688435606E072-27845
chr128843564988435764E072-27687
chr128843582588436088E072-27363
chr128843615588436235E072-27216
chr128844804788448087E072-15364
chr128843582588436088E073-27363
chr128843615588436235E073-27216
chr128845182688451912E073-11539
chr128843085588430978E074-32473
chr128843556688435606E074-27845
chr128843564988435764E074-27687
chr128843582588436088E074-27363
chr128843615588436235E074-27216
chr128843085588430978E081-32473
chr128843109188431135E081-32316
chr128843118388431252E081-32199
chr128843085588430978E082-32473
chr128843109188431135E082-32316
chr128843118388431252E082-32199
chr128843125488431334E082-32117
chr128843154688431586E082-31865
chr128843206788432111E082-31340










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr128842863888428842E067-34609
chr128842885288430682E067-32769
chr128842863888428842E068-34609
chr128842885288430682E068-32769
chr128842863888428842E069-34609
chr128842885288430682E069-32769
chr128842863888428842E070-34609
chr128842885288430682E070-32769
chr128842863888428842E071-34609
chr128842885288430682E071-32769
chr128842863888428842E072-34609
chr128842885288430682E072-32769
chr128842863888428842E073-34609
chr128842885288430682E073-32769
chr128842863888428842E074-34609
chr128842885288430682E074-32769
chr128842863888428842E081-34609
chr128842885288430682E081-32769
chr128842863888428842E082-34609
chr128842885288430682E082-32769