rs5742629

Homo sapiens
T>C
IGF1 : Intron Variant
LOC105369942 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0334 (10003/29924,GnomAD)
C=0333 (9714/29118,TOPMED)
C=0343 (1719/5008,1000G)
C=0274 (1057/3854,ALSPAC)
C=0270 (1001/3708,TWINSUK)
chr12:102463485 (GRCh38.p7) (12q23.2)
AD
GWASdb2
6   publication(s)
See rs on genome
19 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.102463485T>C
GRCh37.p13 chr 12NC_000012.11:g.102857263T>C
IGF1 RefSeqGeneNG_011713.1:g.22116A>G

Gene: IGF1, insulin like growth factor 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
IGF1 transcript variant 4NM_000618.4:c.N/AIntron Variant
IGF1 transcript variant 1NM_001111283.2:c.N/AIntron Variant
IGF1 transcript variant 2NM_001111284.1:c.N/AIntron Variant
IGF1 transcript variant X1XM_017019259.1:c.N/AIntron Variant
IGF1 transcript variant X2XM_017019260.1:c.N/AIntron Variant
IGF1 transcript variant X2XM_017019261.1:c.N/AIntron Variant
IGF1 transcript variant X4XM_017019262.1:c.N/AIntron Variant
IGF1 transcript variant X5XM_017019263.1:c.N/AIntron Variant

Gene: LOC105369942, uncharacterized LOC105369942(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02456 transcript variant X1XR_001749285.1:n....XR_001749285.1:n.3892T>CT>CNon Coding Transcript Variant
LINC02456 transcript variant X2XR_001749286.1:n.N/AGenic Downstream Transcript Variant
LINC02456 transcript variant X3XR_001749287.1:n.N/AGenic Downstream Transcript Variant
LINC02456 transcript variant X4XR_001749288.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.567C=0.433
1000GenomesAmericanSub694T=0.770C=0.230
1000GenomesEast AsianSub1008T=0.573C=0.427
1000GenomesEuropeSub1006T=0.730C=0.270
1000GenomesGlobalStudy-wide5008T=0.657C=0.343
1000GenomesSouth AsianSub978T=0.710C=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.726C=0.274
The Genome Aggregation DatabaseAfricanSub8708T=0.595C=0.405
The Genome Aggregation DatabaseAmericanSub832T=0.760C=0.240
The Genome Aggregation DatabaseEast AsianSub1618T=0.550C=0.450
The Genome Aggregation DatabaseEuropeSub18464T=0.703C=0.296
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.665C=0.334
The Genome Aggregation DatabaseOtherSub302T=0.760C=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.666C=0.333
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.730C=0.270
PMID Title Author Journal
24149131Candidate gene analysis in israeli soldiers with stress fractures.Yanovich RJ Sports Sci Med
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res
21915365Prospective study of insulin-like growth factor-I, insulin-like growth factor-binding protein 3, genetic variants in the IGF1 and IGFBP3 genes and risk of coronary artery disease.Ricketts SLInt J Mol Epidemiol Genet
20435602Genetic association of insulin-like growth factor-1 polymorphisms with high-grade myopia in an international family cohort.Metlapally RInvest Ophthalmol Vis Sci
22509095Association of insulin-like growth factor-1 polymorphisms with high myopia in the Chinese population.Zhuang WMol Vis
19252927Bladder cancer SNP panel predicts susceptibility and survival.Andrew ASHum Genet

P-Value

SNP ID p-value Traits Study
rs57426297E-05alcohol consumption23953852

eQTL of rs5742629 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 rs5742629 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 )
chr12102874086102874984E06916823
chr12102820236102820292E070-36971
chr12102820422102821292E070-35971
chr12102821319102821809E070-35454
chr12102862189102862985E0704926
chr12102820422102821292E071-35971
chr12102821319102821809E071-35454
chr12102874086102874984E07116823
chr12102896212102896262E07138949
chr12102820422102821292E081-35971
chr12102821319102821809E081-35454
chr12102819876102820031E082-37232
chr12102820084102820134E082-37129
chr12102820236102820292E082-36971
chr12102820422102821292E082-35971
chr12102832749102832966E082-24297
chr12102833054102833117E082-24146
chr12102833136102834185E082-23078
chr12102862189102862985E0824926





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12102873731102874032E06716468
chr12102873731102874032E06916468
chr12102873731102874032E07116468
chr12102873731102874032E07216468
chr12102873731102874032E07316468
chr12102873731102874032E08116468