chr2:48751020:A>G Detail (hg38) (LHCGR, STON1-GTF2A1L)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:48,978,159-48,978,159 View the variant detail on this assembly version. |
| hg38 | chr2:48,751,020-48,751,020 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000233.3:c.161+4491T>C | |
| Ensemble | ENST00000294954.12:c.161+4491T>C | |
| ENST00000401907.5:c.161+4491T>C |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001198593.1:c.3442-25260A>G | |
| Ensemble | ENST00000402114.6:c.3442-25260A>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.299 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.130 | polycystic ovary syndrome | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| 0.125 | polycystic ovary syndrome | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| 0.130 | polycystic ovary syndrome | Genome-wide association study identifies susceptibility loci for polycystic ovar... | GWASCAT | 21151128 | Detail |
| 0.120 | polycystic ovary syndrome | Genome-wide association study identifies susceptibility loci for polycystic ovar... | GWASCAT | 21151128 | Detail |
| 0.130 | polycystic ovary syndrome | Genome-wide association study identifies eight new risk loci for polycystic ovar... | GWASCAT | 22885925 | Detail |
| 0.120 | polycystic ovary syndrome | Genome-wide association study identifies eight new risk loci for polycystic ovar... | GWASCAT | 22885925 | Detail |
| 0.123 | polycystic ovary syndrome | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| <0.001 | endometrial carcinoma | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| 0.130 | polycystic ovary syndrome | [Genome-wide association study identifies susceptibility loci for polycystic ova... | GAD | 21151128 | Detail |
| <0.001 | endometrial carcinoma | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| <0.001 | endometrial carcinoma | The aim of this study was to explore the polycystic ovary syndrome (PCOS) relate... | BeFree | 22902918 | Detail |
| <0.001 | Ovarian Diseases | In a previous genome-wide association study, the SNP variants rs13429458, rs1247... | BeFree | 23208300 | Detail |
| 0.003 | hyperandrogenism | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | anovulation | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | hyperandrogenism | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | hyperandrogenism | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | anovulation | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| 0.007 | hyperandrogenism | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | hyperandrogenism | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | anovulation | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | anovulation | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
| <0.001 | anovulation | After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotr... | BeFree | 25586784 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromo... | DisGeNET | Detail |
| Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromo... | DisGeNET | Detail |
| Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. | DisGeNET | Detail |
| Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. | DisGeNET | Detail |
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| [Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chrom... | DisGeNET | Detail |
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| The aim of this study was to explore the polycystic ovary syndrome (PCOS) related single nucleotide ... | DisGeNET | Detail |
| In a previous genome-wide association study, the SNP variants rs13429458, rs12478601, rs2479106, rs1... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
| After adjustment for age and BMI, variants in luteinizing hormone/choriogonadotropin receptor (LHCGR... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs13405728 dbSNP
- Genome
- hg38
- Position
- chr2:48,751,020-48,751,020
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs13405728
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2992
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 5015
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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