rs1336798

Homo sapiens
T>C
OLFM3 : Intron Variant
DNAJA1P5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0226 (6764/29834,GnomAD)
C=0258 (7514/29118,TOPMED)
C=0190 (951/5008,1000G)
C=0272 (1049/3854,ALSPAC)
C=0273 (1012/3708,TWINSUK)
chr1:101886314 (GRCh38.p7) (1p21.1)
ND
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.101886314T>C
GRCh37.p13 chr 1NC_000001.10:g.102351870T>C

Gene: OLFM3, olfactomedin 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
OLFM3 transcript variant 3NM_001288823.1:c.N/AIntron Variant
OLFM3 transcript variant 2NM_058170.3:c.N/AIntron Variant
OLFM3 transcript variant 1NM_001288821.1:c.N/AGenic Upstream Transcript Variant
OLFM3 transcript variant 4NR_110210.1:n.N/AIntron Variant
OLFM3 transcript variant 5NR_110211.1:n.N/AIntron Variant
OLFM3 transcript variant 6NR_110212.1:n.N/AGenic Upstream Transcript Variant
OLFM3 transcript variant X1XM_017000240.1:c.N/AGenic Upstream Transcript Variant

Gene: DNAJA1P5, DnaJ heat shock protein family (Hsp40) member A1 pseudogene 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
DNAJA1P5 transcriptNR_033424.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.703C=0.297
1000GenomesAmericanSub694T=0.800C=0.200
1000GenomesEast AsianSub1008T=0.981C=0.019
1000GenomesEuropeSub1006T=0.734C=0.266
1000GenomesGlobalStudy-wide5008T=0.810C=0.190
1000GenomesSouth AsianSub978T=0.860C=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.728C=0.272
The Genome Aggregation DatabaseAfricanSub8702T=0.709C=0.291
The Genome Aggregation DatabaseAmericanSub838T=0.840C=0.160
The Genome Aggregation DatabaseEast AsianSub1578T=0.990C=0.010
The Genome Aggregation DatabaseEuropeSub18414T=0.782C=0.217
The Genome Aggregation DatabaseGlobalStudy-wide29834T=0.773C=0.226
The Genome Aggregation DatabaseOtherSub302T=0.730C=0.270
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.741C=0.258
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.727C=0.273
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs13367983.74E-05nicotine dependence (smoking)22377092

eQTL of rs1336798 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 rs1336798 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 )
chr1102314583102314682E070-37188
chr1102314900102315460E070-36410
chr1102381450102381705E07029580
chr1102367700102368361E08115830
chr1102368465102368524E08116595


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1102312291102312873E067-38997
chr1102312291102312873E068-38997
chr1102312291102312873E070-38997
chr1102312291102312873E072-38997
chr1102312291102312873E073-38997
chr1102312291102312873E082-38997