rs1522153

Homo sapiens
G>A
NEK10 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0336 (10069/29914,GnomAD)
G==0345 (10068/29118,TOPMED)
G==0304 (1521/5008,1000G)
G==0317 (1223/3854,ALSPAC)
G==0285 (1055/3708,TWINSUK)
chr3:27129286 (GRCh38.p7) (3p24.1)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.27129286G>A
GRCh37.p13 chr 3NC_000003.11:g.27170777G>A

Gene: NEK10, NIMA related kinase 10(minus strand)

Molecule type Change Amino acid[Codon] SO Term
NEK10 transcript variant 1NM_001031741.3:c.N/AIntron Variant
NEK10 transcript variant 4NM_001304384.1:c.N/AIntron Variant
NEK10 transcript variant 2NM_152534.4:c.N/AIntron Variant
NEK10 transcript variant 3NM_199347.3:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X7XM_006712997.3:c.N/AIntron Variant
NEK10 transcript variant X9XM_006712998.2:c.N/AIntron Variant
NEK10 transcript variant X10XM_006712999.3:c.N/AIntron Variant
NEK10 transcript variant X16XM_006713001.3:c.N/AIntron Variant
NEK10 transcript variant X2XM_017005761.1:c.N/AIntron Variant
NEK10 transcript variant X3XM_017005762.1:c.N/AIntron Variant
NEK10 transcript variant X4XM_017005763.1:c.N/AIntron Variant
NEK10 transcript variant X5XM_017005764.1:c.N/AIntron Variant
NEK10 transcript variant X6XM_017005765.1:c.N/AIntron Variant
NEK10 transcript variant X8XM_017005766.1:c.N/AIntron Variant
NEK10 transcript variant X11XM_017005767.1:c.N/AIntron Variant
NEK10 transcript variant X13XM_017005768.1:c.N/AIntron Variant
NEK10 transcript variant X14XM_017005769.1:c.N/AIntron Variant
NEK10 transcript variant X14XM_017005770.1:c.N/AIntron Variant
NEK10 transcript variant X16XM_017005771.1:c.N/AIntron Variant
NEK10 transcript variant X17XM_017005772.1:c.N/AIntron Variant
NEK10 transcript variant X23XM_006713002.1:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X20XM_011533413.2:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X24XM_011533414.2:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X25XM_011533415.1:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X19XM_017005773.1:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X20XM_017005774.1:c.N/AGenic Downstream Transcript Variant
NEK10 transcript variant X1XR_001740034.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.511A=0.489
1000GenomesAmericanSub694G=0.210A=0.790
1000GenomesEast AsianSub1008G=0.177A=0.823
1000GenomesEuropeSub1006G=0.294A=0.706
1000GenomesGlobalStudy-wide5008G=0.304A=0.696
1000GenomesSouth AsianSub978G=0.230A=0.770
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.317A=0.683
The Genome Aggregation DatabaseAfricanSub8698G=0.455A=0.545
The Genome Aggregation DatabaseAmericanSub836G=0.180A=0.820
The Genome Aggregation DatabaseEast AsianSub1618G=0.144A=0.856
The Genome Aggregation DatabaseEuropeSub18462G=0.306A=0.693
The Genome Aggregation DatabaseGlobalStudy-wide29914G=0.336A=0.663
The Genome Aggregation DatabaseOtherSub300G=0.210A=0.790
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.345A=0.654
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.285A=0.715
PMID Title Author Journal
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs15221533E-06alcohol dependence21956439

eQTL of rs1522153 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 rs1522153 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 )
chr32712328327123473E072-47304
chr32712328327123473E074-47304
chr32712353727123778E074-46999
chr32720572227205808E08134945
chr32720845927208739E08137682
chr32720878427208894E08138007
chr32720894527208995E08138168
chr32712380427123983E082-46794
chr32720894527208995E08238168