rs1060061

Homo sapiens
T>C
NR5A2 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0432 (12935/29898,GnomAD)
T==0413 (12042/29118,TOPMED)
C=0463 (2320/5008,1000G)
T==0449 (1732/3854,ALSPAC)
T==0439 (1629/3708,TWINSUK)
chr1:200174314 (GRCh38.p7) (1q32.1)
ND
GWASCatalog
2   publication(s)
See rs on genome
12 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.200174314T>C
GRCh37.p13 chr 1NC_000001.10:g.200143442T>C

Gene: NR5A2, nuclear receptor subfamily 5 group A member 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NR5A2 transcript variant 1NM_205860.2:c.N/A3 Prime UTR Variant
NR5A2 transcript variant 2NM_003822.4:c.N/A3 Prime UTR Variant
NR5A2 transcript variant 3NM_001276464.1:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X1XM_011509380.1:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X4XM_011509382.1:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X2XM_017000904.1:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X3XM_011509381.2:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X5XM_005245062.3:c.N/A3 Prime UTR Variant
NR5A2 transcript variant X6XM_011509384.2:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.310C=0.690
1000GenomesAmericanSub694T=0.490C=0.510
1000GenomesEast AsianSub1008T=0.912C=0.088
1000GenomesEuropeSub1006T=0.433C=0.567
1000GenomesGlobalStudy-wide5008T=0.537C=0.463
1000GenomesSouth AsianSub978T=0.600C=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.449C=0.551
The Genome Aggregation DatabaseAfricanSub8714T=0.328C=0.672
The Genome Aggregation DatabaseAmericanSub834T=0.510C=0.490
The Genome Aggregation DatabaseEast AsianSub1614T=0.914C=0.086
The Genome Aggregation DatabaseEuropeSub18434T=0.436C=0.563
The Genome Aggregation DatabaseGlobalStudy-wide29898T=0.432C=0.567
The Genome Aggregation DatabaseOtherSub302T=0.420C=0.580
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.413C=0.586
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.439C=0.561
PMID Title Author Journal
24200957Irritable bowel syndrome-diarrhea: characterization of genotype by exome sequencing, and phenotypes of bile acid synthesis and colonic transit.Camilleri MAm J Physiol Gastrointest Liver Physiol
28440896Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.Yin XAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs10600614E-06nicotine dependence28440896

eQTL of rs1060061 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 rs1060061 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 )
chr1200098374200098983E069-44459
chr1200098374200098983E072-44459
chr1200098374200098983E074-44459
chr1200099053200099106E074-44336
chr1200141490200141908E081-1534
chr1200141993200142343E081-1099
chr1200142396200142480E081-962
chr1200142484200142580E081-862
chr1200143131200143237E081-205
chr1200142396200142480E082-962
chr1200142484200142580E082-862
chr1200143131200143237E082-205