rs1552859

Homo sapiens
G>T
NELL2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0389 (11538/29612,GnomAD)
T=0309 (8999/29118,TOPMED)
T=0415 (2078/5008,1000G)
T=0445 (1715/3854,ALSPAC)
T=0449 (1665/3708,TWINSUK)
chr12:44537118 (GRCh38.p7) (12q12)
AD
GWASdb2
1   publication(s)
See rs on genome
20 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.44537118G>T
GRCh37.p13 chr 12NC_000012.11:g.44930901G>T

Gene: NELL2, neural EGFL like 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
NELL2 transcript variant 1NM_001145107.1:c.N/AIntron Variant
NELL2 transcript variant 3NM_001145108.1:c.N/AIntron Variant
NELL2 transcript variant 4NM_001145109.1:c.N/AIntron Variant
NELL2 transcript variant 5NM_001145110.1:c.N/AIntron Variant
NELL2 transcript variant 2NM_006159.2:c.N/AIntron Variant
NELL2 transcript variant X6XM_005268905.3:c.N/AIntron Variant
NELL2 transcript variant X5XM_011538396.1:c.N/AIntron Variant
NELL2 transcript variant X1XM_017019341.1:c.N/AIntron Variant
NELL2 transcript variant X2XM_017019342.1:c.N/AIntron Variant
NELL2 transcript variant X3XM_017019343.1:c.N/AIntron Variant
NELL2 transcript variant X4XM_017019344.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.937T=0.063
1000GenomesAmericanSub694G=0.500T=0.500
1000GenomesEast AsianSub1008G=0.321T=0.679
1000GenomesEuropeSub1006G=0.580T=0.420
1000GenomesGlobalStudy-wide5008G=0.585T=0.415
1000GenomesSouth AsianSub978G=0.450T=0.550
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.555T=0.445
The Genome Aggregation DatabaseAfricanSub8654G=0.873T=0.127
The Genome Aggregation DatabaseAmericanSub824G=0.450T=0.550
The Genome Aggregation DatabaseEast AsianSub1610G=0.339T=0.661
The Genome Aggregation DatabaseEuropeSub18222G=0.517T=0.482
The Genome Aggregation DatabaseGlobalStudy-wide29612G=0.610T=0.389
The Genome Aggregation DatabaseOtherSub302G=0.570T=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.690T=0.309
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.551T=0.449
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs15528590.00074alcohol dependence24277619

eQTL of rs1552859 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 rs1552859 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 )
chr124491378944913851E068-17050
chr124491391744913997E068-16904
chr124491402944914128E068-16773
chr124490136644901828E070-29073
chr124490218744902227E070-28674
chr124490236044902414E070-28487
chr124491378944913851E071-17050
chr124491391744913997E071-16904
chr124491378944913851E072-17050
chr124491391744913997E072-16904
chr124491402944914128E072-16773
chr124491378944913851E074-17050
chr124491391744913997E074-16904
chr124491402944914128E074-16773
chr124492535644925480E081-5421
chr124492549244925578E081-5323
chr124492560044925737E081-5164
chr124493428944934412E0813388
chr124490136644901828E082-29073
chr124491391744913997E082-16904