chr17:54979110:G>A Detail (hg38) (STXBP4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:53,056,471-53,056,471 View the variant detail on this assembly version. |
| hg38 | chr17:54,979,110-54,979,110 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_178509.5:c.-156-6504G>A | |
| Ensemble | ENST00000376352.6:c.-156-6504G>A | |
| ENST00000398391.6:c.-254-6504G>A |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.053 | |
| 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 |
|---|---|---|---|---|---|
| <0.001 | breast carcinoma | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| 0.132 | Malignant neoplasm of breast | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| 0.001 | breast carcinoma | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| 0.001 | Malignant neoplasm of breast | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| 0.003 | breast carcinoma | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| 0.123 | Malignant neoplasm of breast | We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... | BeFree | 21791674 | Detail |
| <0.001 | Malignant neoplasm of female breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | Carcinoma of male breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | female breast carcinoma | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | Malignant neoplasm of male breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | Malignant neoplasm of male breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | female breast carcinoma | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | Carcinoma of male breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | Malignant neoplasm of female breast | Comparing the ORs for male breast cancer with the published ORs for female breas... | BeFree | 21949660 | Detail |
| <0.001 | breast carcinoma | Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer r... | BeFree | 22863968 | Detail |
| 0.128 | Malignant neoplasm of breast | Large-scale genotyping identifies 41 new loci associated with breast cancer risk... | GWASCAT | 23535729 | Detail |
| 0.001 | Malignant neoplasm of breast | Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer r... | BeFree | 22863968 | Detail |
| 0.001 | breast carcinoma | Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer r... | BeFree | 22863968 | Detail |
| 0.128 | Malignant neoplasm of breast | Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer r... | BeFree | 22863968 | Detail |
| 0.006 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.131 | Malignant neoplasm of breast | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.031 | breast carcinoma | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.009 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.031 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.001 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.162 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.002 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.001 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.162 | Malignant neoplasm of breast | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.002 | breast carcinoma | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.004 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.170 | Malignant neoplasm of breast | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.131 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.230 | Malignant neoplasm of breast | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| <0.001 | breast carcinoma | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.049 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.166 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.128 | Malignant neoplasm of breast | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.090 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.004 | breast carcinoma | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
| 0.019 | breast carcinoma | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.230 | Malignant neoplasm of breast | Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... | BeFree | 22532573 | Detail |
| 0.010 | breast carcinoma | We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941... | BeFree | 23893088 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Comparing the ORs for male breast cancer with the published ORs for female breast cancer, three SNPs... | DisGeNET | Detail |
| Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 1... | DisGeNET | Detail |
| Large-scale genotyping identifies 41 new loci associated with breast cancer risk. | DisGeNET | Detail |
| Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 1... | DisGeNET | Detail |
| Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 1... | DisGeNET | Detail |
| Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 1... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... | DisGeNET | Detail |
| We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs298158... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs6504950 dbSNP
- Genome
- hg38
- Position
- chr17:54,979,110-54,979,110
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- 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))
- rs6504950
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0527
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 884
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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