rs1554368

Homo sapiens
A>G
NELL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0211 (6333/29926,GnomAD)
A==0254 (7397/29118,TOPMED)
A==0200 (1000/5008,1000G)
A==0181 (699/3854,ALSPAC)
A==0191 (707/3708,TWINSUK)
chr11:20754212 (GRCh38.p7) (11p15.1)
ND
GWASdb2
1   publication(s)
See rs on genome
43 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.20754212A>G
GRCh37.p13 chr 11NC_000011.9:g.20775758A>G

Gene: NELL1, neural EGFL like 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NELL1 transcript variant 3NM_001288713.1:c.N/AIntron Variant
NELL1 transcript variant 4NM_001288714.1:c.N/AIntron Variant
NELL1 transcript variant 1NM_006157.4:c.N/AIntron Variant
NELL1 transcript variant 2NM_201551.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.348G=0.652
1000GenomesAmericanSub694A=0.170G=0.830
1000GenomesEast AsianSub1008A=0.119G=0.881
1000GenomesEuropeSub1006A=0.176G=0.824
1000GenomesGlobalStudy-wide5008A=0.200G=0.800
1000GenomesSouth AsianSub978A=0.130G=0.870
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.181G=0.819
The Genome Aggregation DatabaseAfricanSub8700A=0.318G=0.682
The Genome Aggregation DatabaseAmericanSub836A=0.190G=0.810
The Genome Aggregation DatabaseEast AsianSub1614A=0.100G=0.900
The Genome Aggregation DatabaseEuropeSub18474A=0.172G=0.827
The Genome Aggregation DatabaseGlobalStudy-wide29926A=0.211G=0.788
The Genome Aggregation DatabaseOtherSub302A=0.180G=0.820
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.254G=0.746
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.191G=0.809
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs15543680.000835nicotine smoking19268276

eQTL of rs1554368 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 rs1554368 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 )
chr112079204720792372E06916289
chr112078382220784011E0708064
chr112078408420784261E0708326
chr112078463820784747E0708880
chr112078476020784810E0709002
chr112079204720792372E07016289
chr112079293320793011E07017175
chr112079306420793259E07017306
chr112079331420793378E07017556
chr112079344520793495E07017687
chr112079353220793582E07017774
chr112079368820793859E07017930
chr112080443820804488E07028680
chr112080451120804669E07028753
chr112080485620805051E07029098
chr112080525520805332E07029497
chr112078206020782143E0716302
chr112078229520782654E0716537
chr112078339220783442E0717634
chr112078352420783579E0717766
chr112079204720792372E07116289
chr112079293320793011E07117175
chr112078268620782736E0726928
chr112078310220783216E0727344
chr112078339220783442E0727634
chr112078352420783579E0727766
chr112078268620782736E0746928
chr112079204720792372E07416289
chr112073709620737316E081-38442
chr112073748020737835E081-37923
chr112073790620737956E081-37802
chr112078206020782143E0816302
chr112078229520782654E0816537
chr112078268620782736E0816928
chr112078463820784747E0818880
chr112078476020784810E0819002
chr112080451120804669E08128753
chr112080485620805051E08129098
chr112080525520805332E08129497
chr112080443820804488E08228680
chr112080451120804669E08228753
chr112080485620805051E08229098
chr112080525520805332E08229497