rs5998935

Homo sapiens
G>A / G>C
LARGE : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0412 (12337/29940,GnomAD)
G==0402 (11714/29114,TOPMED)
G==0497 (2489/5008,1000G)
G==0398 (1534/3854,ALSPAC)
G==0399 (1478/3708,TWINSUK)
chr22:33411849 (GRCh38.p7) (22q12.3)
ND
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.33411849G>A
GRCh38.p7 chr 22NC_000022.11:g.33411849G>C
GRCh37.p13 chr 22NC_000022.10:g.33807835G>A
GRCh37.p13 chr 22NC_000022.10:g.33807835G>C
LARGE1 RefSeqGeneNG_009929.2:g.513580C>T
LARGE1 RefSeqGeneNG_009929.2:g.513580C>G

Gene: LARGE, like-glycosyltransferase(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LARGE1 transcript variant 1NM_004737.4:c.N/AIntron Variant
LARGE1 transcript variant 2NM_133642.3:c.N/AIntron Variant
LARGE1 transcript variant X1XM_005261831.3:c.N/AIntron Variant
LARGE1 transcript variant X3XM_005261832.3:c.N/AIntron Variant
LARGE1 transcript variant X2XM_011530510.2:c.N/AIntron Variant
LARGE1 transcript variant X6XM_011530512.2:c.N/AIntron Variant
LARGE transcript variant X7XM_011530514.2:c.N/AIntron Variant
LARGE1 transcript variant X7XM_011530513.2:c.N/AGenic Upstream Transcript Variant
LARGE transcript variant X4XR_001755370.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.380A=0.620
1000GenomesAmericanSub694G=0.360A=0.640
1000GenomesEast AsianSub1008G=0.721A=0.279
1000GenomesEuropeSub1006G=0.442A=0.558
1000GenomesGlobalStudy-wide5008G=0.497A=0.503
1000GenomesSouth AsianSub978G=0.580A=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.398A=0.602
The Genome Aggregation DatabaseAfricanSub8706G=0.403C=0.000
The Genome Aggregation DatabaseAmericanSub838G=0.410C=0.00,
The Genome Aggregation DatabaseEast AsianSub1616G=0.691C=0.000
The Genome Aggregation DatabaseEuropeSub18478G=0.389C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29940G=0.412C=0.000
The Genome Aggregation DatabaseOtherSub302G=0.550C=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29114G=0.402A=0.597
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.399A=0.601
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
rs59989359.37E-05nicotine smoking19268276

eQTL of rs5998935 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 rs5998935 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 )
chr222306397223064154E07136305
chr222306397223064154E07236305
chr222299480922995169E081-32498
chr222299525922995409E081-32258
chr222302644723026501E081-1166
chr222302653623026596E081-1071
chr222302693023026980E081-687
chr222302699723027502E081-165
chr222302754323027993E0810
chr222305130623051572E08123639
chr222305175523051854E08124088
chr222305189123051981E08124224
chr222302516923025209E082-2458
chr222302523023025324E082-2343
chr222302556223025633E082-2034