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SNP Detail For rs646776
1.Mapping Information
| Human SNP ID | rs646776 |
|---|---|
| Human chromosome | chr1 |
| Human SNP position | 109275908 |
| Pig chromosome | chr4 |
| Pig SNP position | 121295578 |
2.Annotation Information
| PubMed ID | 19060911 |
|---|---|
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060911 |
| Study | Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. |
| Disease/Trait | Cholesterol, total |
| Initial sample | 21,848 European ancestry individuals, 714 Orcadian individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-G |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 9E-22 |
| Pvalue mlog | 21.0457574905606 |
| P value text | |
| Or beta | 0.13 |
| %95 Ci | [NR] s.d. decrease |
| Platform | Affymetrix, Illumina [up to 600000] |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST000285 |
| PubMed ID | 19060911 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060911 |
| Study | Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 17,083 European ancestry individuals, 714 Orcadian individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-G |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 8E-23 |
| Pvalue mlog | 22.096910013008 |
| P value text | |
| Or beta | 0.16 |
| %95 Ci | [NR] s.d. decrease |
| Platform | Affymetrix, Illumina [up to 600000] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000282 |
| PubMed ID | 19060910 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19060910 |
| Study | Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 4,763 Northern Finnish founder individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-G |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.21 |
| P value | 0.000000000002 |
| Pvalue mlog | 11.698970004336 |
| P value text | |
| Or beta | 0.16 |
| %95 Ci | [0.11-0.20] mmol/l decrease |
| Platform | Illumina [329091] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000283 |
| PubMed ID | 19198609 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19198609 |
| Study | Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. |
| Disease/Trait | Myocardial infarction (early onset) |
| Initial sample | 2,967 European ancestry cases, 3,075 European ancestry controls |
| Replication sample | 9,746 European ancestry cases, 9,746 European ancestry controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-T |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.81 |
| P value | 0.000000000008 |
| Pvalue mlog | 11.096910013008 |
| P value text | |
| Or beta | 1.19 |
| %95 Ci | [1.13-1.26] |
| Platform | Affymetrix [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | myocardial infarction |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000612 |
| Study accession | GCST000340 |
| PubMed ID | 21087763 |
| Journal | Am J Hum Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21087763 |
| Study | Genome-wide screen identifies rs646776 near sortilin as a regulator of progranulin levels in human plasma. |
| Disease/Trait | Progranulin levels |
| Initial sample | 518 European ancestry controls |
| Replication sample | 459 European ancestry controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-G |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.21 |
| P value | 2E-30 |
| Pvalue mlog | 29.698970004336 |
| P value text | |
| Or beta | 0.18 |
| %95 Ci | [0.16-0.20] ng/ml decrease |
| Platform | Illumina [313504] |
| CNV | N |
| Mapped trait | progranulin measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004625 |
| Study accession | GCST000911 |
| PubMed ID | 21378988 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21378988 |
| Study | A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease. |
| Disease/Trait | Coronary heart disease |
| Initial sample | 8,424 European ancestry cases, 7,268 European ancestry controls, 6,996 South Asian ancestry cases, 7,794 South Asian ancestry controls |
| Replication sample | 18,049 European ancestry cases, 16,357 European ancestry controls, 3,359 South Asian ancestry cases, 2,828 South Asian ancestry controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-T |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000000006 |
| Pvalue mlog | 9.22184874961635 |
| P value text | |
| Or beta | 1.14 |
| %95 Ci | [1.09-1.19] |
| Platform | Illumina [574919] |
| CNV | N |
| Mapped trait | coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST000999 |
| PubMed ID | 20339536 |
| Journal | PLoS One |
| Link | www.ncbi.nlm.nih.gov/pubmed/20339536 |
| Study | Genome-wide association of lipid-lowering response to statins in combined study populations. |
| Disease/Trait | Response to statin therapy |
| Initial sample | 3,928 European ancestry individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-C |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.19 |
| P value | 0.000004 |
| Pvalue mlog | 5.39794000867203 |
| P value text | (chol, sum) |
| Or beta | |
| %95 Ci | |
| Platform | Illumina [~ 2500000] (imputed) |
| CNV | N |
| Mapped trait | response to statin |
| Mapped trait URI | http://purl.obolibrary.org/obo/GO_0036273 |
| Study accession | GCST000635 |
| PubMed ID | 19936222 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19936222 |
| Study | Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. |
| Disease/Trait | Lipid metabolism phenotypes |
| Initial sample | Up to 17,296 European ancestry female individuals |
| Replication sample | Up to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SPRT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-? |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 2E-53 |
| Pvalue mlog | 52.698970004336 |
| P value text | (APOB.assay, whole) |
| Or beta | 5.205 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [335603] |
| CNV | N |
| Mapped trait | lipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004529 |
| Study accession | GCST000533 |
| PubMed ID | 19936222 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19936222 |
| Study | Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. |
| Disease/Trait | Lipid metabolism phenotypes |
| Initial sample | Up to 17,296 European ancestry female individuals |
| Replication sample | Up to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SPRT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-? |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 4E-39 |
| Pvalue mlog | 38.397940008672 |
| P value text | (APOB.assay, fasting) |
| Or beta | 5.251 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [335603] |
| CNV | N |
| Mapped trait | lipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004529 |
| Study accession | GCST000533 |
| PubMed ID | 19936222 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19936222 |
| Study | Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. |
| Disease/Trait | Lipid metabolism phenotypes |
| Initial sample | Up to 17,296 European ancestry female individuals |
| Replication sample | Up to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SPRT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-? |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 2E-20 |
| Pvalue mlog | 19.698970004336 |
| P value text | (LDL.total, fasting) |
| Or beta | 0.043 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [335603] |
| CNV | N |
| Mapped trait | lipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004529 |
| Study accession | GCST000533 |
| PubMed ID | 19936222 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19936222 |
| Study | Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. |
| Disease/Trait | Lipid metabolism phenotypes |
| Initial sample | Up to 17,296 European ancestry female individuals |
| Replication sample | Up to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, PSRC1, SPRT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-? |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 2E-27 |
| Pvalue mlog | 26.698970004336 |
| P value text | (LDL.total, whole) |
| Or beta | 0.042 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [335603] |
| CNV | N |
| Mapped trait | lipid measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004529 |
| Study accession | GCST000533 |
| PubMed ID | 21239051 |
| Journal | Lancet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21239051 |
| Study | Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. |
| Disease/Trait | Coronary artery disease |
| Initial sample | 1,808 European ancestry cases, 915 European ancestry controls |
| Replication sample | 10,585 European ancestry cases, 6,468 European ancestry controls |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-T |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.79 |
| P value | 0.00000000008 |
| Pvalue mlog | 10.096910013008 |
| P value text | |
| Or beta | 1.33 |
| %95 Ci | [1.22-1.44] |
| Platform | Affymetrix, Illumina [> 2400000] (imputed) |
| CNV | N |
| Mapped trait | coronary heart disease |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001645 |
| Study accession | GCST000945 |
| PubMed ID | 18193044 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/18193044 |
| Study | Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. |
| Disease/Trait | LDL cholesterol |
| Initial sample | 2,758 European ancestry individuals |
| Replication sample | 18,544 European ancestry individuals |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | PSRC1, CELSR2, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-C |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.24 |
| P value | 3E-29 |
| Pvalue mlog | 28.5228787452803 |
| P value text | |
| Or beta | 0.16 |
| %95 Ci | [0.14-0.18] percentage SD decrease |
| Platform | Affymetrix [389878] |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST000134 |
| PubMed ID | 25961943 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25961943 |
| Study | The impact of low-frequency and rare variants on lipid levels. |
| Disease/Trait | Cholesterol, total |
| Initial sample | up to 62,166 European ancestry individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-T |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 2E-64 |
| Pvalue mlog | 63.698970004336 |
| P value text | |
| Or beta | 0.12 |
| %95 Ci | [0.11-0.13] s.d. increase |
| Platform | Affymetrix, Illumina, Perlegen [up to 9657952] (imputed) |
| CNV | N |
| Mapped trait | total cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004574 |
| Study accession | GCST002896 |
| PubMed ID | 25961943 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/25961943 |
| Study | The impact of low-frequency and rare variants on lipid levels. |
| Disease/Trait | LDL cholesterol |
| Initial sample | up 62,166 European ancestry individuals |
| Replication sample | NA |
| Region | 1p13.3 |
| Chromosome id | chr1 |
| Chromosome position | 109275908 |
| Reported gene | CELSR2, SORT1 |
| Mapped gene | CELSR2 - PSRC1 |
| Upstream gene id | 1952 |
| Downstream gene id | 84722 |
| SNP gene ids | |
| Upstream gene distance | 152 |
| Downstream gene distance | 3646 |
| SNP risk allele | rs646776-T |
| SNPs | rs646776 |
| Merged | 0 |
| SNP id current | 646776 |
| Context | downstream_gene_variant |
| Intergenic | 1 |
| Allele frequency | 0.22 |
| P value | 2E-91 |
| Pvalue mlog | 90.698970004336 |
| P value text | |
| Or beta | 0.146 |
| %95 Ci | [0.13-0.16] s.d. increase |
| Platform | Affymetrix, Illumina, Perlegen [up to 9657952] (imputed) |
| CNV | N |
| Mapped trait | low density lipoprotein cholesterol measurement |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004611 |
| Study accession | GCST002898 |
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