rs249571

Homo sapiens
C>T
NEDD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0499 (14947/29922,GnomAD)
C==0466 (13568/29118,TOPMED)
C==0441 (2207/5008,1000G)
T=0464 (1788/3854,ALSPAC)
T=0481 (1783/3708,TWINSUK)
chr12:96927433 (GRCh38.p7) (12q23.1)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.96927433C>T
GRCh37.p13 chr 12NC_000012.11:g.97321211C>T

Gene: NEDD1, neural precursor cell expressed, developmentally down-regulated 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NEDD1 transcript variant 1NM_001135175.1:c.N/AIntron Variant
NEDD1 transcript variant 3NM_001135176.1:c.N/AIntron Variant
NEDD1 transcript variant 4NM_001135177.1:c.N/AIntron Variant
NEDD1 transcript variant 2NM_152905.3:c.N/AIntron Variant
NEDD1 transcript variant X1XM_005268644.2:c.N/AIntron Variant
NEDD1 transcript variant X2XM_006719237.3:c.N/AIntron Variant
NEDD1 transcript variant X3XM_011537903.2:c.N/AIntron Variant
NEDD1 transcript variant X4XM_011537904.2:c.N/AIntron Variant
NEDD1 transcript variant X6XM_011537905.2:c.N/AIntron Variant
NEDD1 transcript variant X8XM_011537906.2:c.N/AIntron Variant
NEDD1 transcript variant X5XM_017018801.1:c.N/AIntron Variant
NEDD1 transcript variant X7XM_017018802.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.336T=0.664
1000GenomesAmericanSub694C=0.460T=0.540
1000GenomesEast AsianSub1008C=0.441T=0.559
1000GenomesEuropeSub1006C=0.548T=0.452
1000GenomesGlobalStudy-wide5008C=0.441T=0.559
1000GenomesSouth AsianSub978C=0.460T=0.540
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.536T=0.464
The Genome Aggregation DatabaseAfricanSub8706C=0.395T=0.605
The Genome Aggregation DatabaseAmericanSub834C=0.440T=0.560
The Genome Aggregation DatabaseEast AsianSub1618C=0.454T=0.546
The Genome Aggregation DatabaseEuropeSub18464C=0.556T=0.443
The Genome Aggregation DatabaseGlobalStudy-wide29922C=0.499T=0.500
The Genome Aggregation DatabaseOtherSub300C=0.460T=0.540
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.466T=0.534
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.519T=0.481
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
rs2495710.000768alcohol dependence20201924

eQTL of rs249571 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 rs249571 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 )
chr129730258497302637E070-18574
chr129730258497302637E071-18574


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr129730006797302528E067-18683
chr129730006797302528E068-18683
chr129730006797302528E069-18683
chr129730006797302528E070-18683
chr129730006797302528E071-18683
chr129730006797302528E072-18683
chr129730006797302528E073-18683
chr129730006797302528E074-18683
chr129730006797302528E081-18683
chr129730006797302528E082-18683