rs1996623

Homo sapiens
A>G
NELL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0153 (4567/29852,GnomAD)
G=0129 (3783/29118,TOPMED)
G=0199 (998/5008,1000G)
G=0140 (540/3854,ALSPAC)
G=0140 (518/3708,TWINSUK)
chr11:20737870 (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.20737870A>G
GRCh37.p13 chr 11NC_000011.9:g.20759416A>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=0.886G=0.114
1000GenomesAmericanSub694A=0.770G=0.230
1000GenomesEast AsianSub1008A=0.746G=0.254
1000GenomesEuropeSub1006A=0.854G=0.146
1000GenomesGlobalStudy-wide5008A=0.801G=0.199
1000GenomesSouth AsianSub978A=0.710G=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.860G=0.140
The Genome Aggregation DatabaseAfricanSub8660A=0.872G=0.128
The Genome Aggregation DatabaseAmericanSub836A=0.760G=0.240
The Genome Aggregation DatabaseEast AsianSub1590A=0.743G=0.257
The Genome Aggregation DatabaseEuropeSub18464A=0.848G=0.151
The Genome Aggregation DatabaseGlobalStudy-wide29852A=0.847G=0.153
The Genome Aggregation DatabaseOtherSub302A=0.850G=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.870G=0.129
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.860G=0.140
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
rs19966230.000883nicotine smoking19268276

eQTL of rs1996623 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 rs1996623 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 )
chr112079204720792372E06932631
chr112078382220784011E07024406
chr112078408420784261E07024668
chr112078463820784747E07025222
chr112078476020784810E07025344
chr112079204720792372E07032631
chr112079293320793011E07033517
chr112079306420793259E07033648
chr112079331420793378E07033898
chr112079344520793495E07034029
chr112079353220793582E07034116
chr112079368820793859E07034272
chr112080443820804488E07045022
chr112080451120804669E07045095
chr112080485620805051E07045440
chr112080525520805332E07045839
chr112078206020782143E07122644
chr112078229520782654E07122879
chr112078339220783442E07123976
chr112078352420783579E07124108
chr112079204720792372E07132631
chr112079293320793011E07133517
chr112078268620782736E07223270
chr112078310220783216E07223686
chr112078339220783442E07223976
chr112078352420783579E07224108
chr112078268620782736E07423270
chr112079204720792372E07432631
chr112073709620737316E081-22100
chr112073748020737835E081-21581
chr112073790620737956E081-21460
chr112078206020782143E08122644
chr112078229520782654E08122879
chr112078268620782736E08123270
chr112078463820784747E08125222
chr112078476020784810E08125344
chr112080451120804669E08145095
chr112080485620805051E08145440
chr112080525520805332E08145839
chr112080443820804488E08245022
chr112080451120804669E08245095
chr112080485620805051E08245440
chr112080525520805332E08245839