استخراج اطلاعات واریانت از Ensembl؛ آموزش rsID، MAF و ارتباط بالینی

10 پاسخ

1. VARIANT 1

   rsID: rs7412

   Chromosome: 19

   Position (GRCh38): 19:44908684

   Alleles: C/T

   Minor Allele: T

   Global Allele Frequency / MAF: 0/17

   Highest Population Frequency: 0.172

   Population: Kinh in Ho Chi Minh City, Vietnam

   Allele: T

   Frequency: 0.172

   Associated Gene: APOE

   Consequence: missense variant

   Clinical Significance:

   Benign
   Likely benign

   Associated Phenotype / Disease:
   ClinVar: phenotype not specified
   Blood protein levels
   Alzheimer’s disease

   Information Source: ClinVar

   Access Date: 30/07/2026

   —————————————-

   VARIANT 2

   rsID: rs1760890

   Chromosome: 14

   Position (GRCh38): 14:20413630

   Alleles: C/A/G/T

   Minor Allele: C

   Global Allele Frequency / MAF: 0.143

   Highest Population Frequency: 0.406

   Population: PEL (Peruvians from Lima, Peru)

   Allele: C

   Frequency: 0.406

   Associated Gene: Novel transcript (ENSG00000300624)

   Consequence: intron variant

   Clinical Significance: No clinical significance reported

   Associated Phenotype / Disease: None reported

   Information Source: –

   Access Date: 30/07/2026

   پاسخ

   1. اصلاح جواب :
      VARIANT 1

      Position (GRCh38): 19:44908822

      Global Allele Frequency / MAF: T 0.08 (8%) C: 0.92 (92%)

      Highest Population Frequency: 17%

      —————————————-

      VARIANT 2

      Global Allele Frequency / MAF: 0.16

      Associated Gene: TEP1

      پاسخ

2. تکلیف :rs7412
   MAf:0/17
   19 44908822 (rs7412) CT
   : تکلیف:rs1760890
   MAf(c)0/16
   MAf(T)0/41
   14 20413360 (rs1760890) cA/cT

   پاسخ

3. VARIANT 1

   rsID: 7412

   Chromosome: 19

   Position (GRCh38): 44908822

   Alleles: C/T
   Minor Allele:

   Global Allele Frequency / MAF: 0.17

   Highest Population Frequency: 0.17

   Population: ALL

   Allele:

   Frequency: C:92% T: 8%

   Associated Gene: APOE

   Consequence: missense variant

   Clinical Significance:

   Associated Phenotype / Disease: Alzheimer

   Information Source: 1000 Genomes Project

   Access Date:

   —————————————-

   VARIANT 2

   rsID: 1760890

   Chromosome: 14

   Position (GRCh38): 20413630

   Alleles: C/A/G/T

   Minor Allele: (C)

   Global Allele Frequency / MAF: 0.16

   Highest Population Frequency: 0.41

   Population: ALL
   Allele:
   Frequency:C: 14%
   A: 86%

   Associated Gene: lncRNA

   Consequence: intron variant
   regulatory region variant

   Clinical Significance:

   Associated Phenotype / Disease: breast cancer

   Information Source:

   Access Date:

   پاسخ

   1. اصلاحیه پاسخ :

      VARIANT 1
      Position (GRCh38): 19:44908822
      Minor Allele: T
      —————————————
      VARIANT 2
      Position (GRCh38): 14:20413630
      Associated Gene: TEP1

      پاسخ

4. VARIANT 1

   rsID: rs7412

   Chromosome: 19

   Position (GRCh38): 44908822

   Alleles: C/T

   Minor Allele: T All Population:8%

   Global Allele Frequency / MAF:0/17

   Highest Population Frequency: C:0/925

   Population: All

   Allele: C/T

   Frequency: C|C:0/855(2142) C|T:0/139(348) T|T:0.006(14)

   Associated Gene: C

   Consequence: Missense Variant

   Clinical Significance: –

   Associated Phenotype / Disease: –

   Information Source: ensembl

   Access Date: 8/4/2026

   —————————————-

   VARIANT 2

   rsID: rs1760890

   Chromosome: 14

   Position (GRCh38): 20413630

   Alleles: C/A/G/T

   Minor Allele: C All Population:0/143

   Global Allele Frequency / MAF: 0/41

   Highest Population Frequency: All Population : A:0/857

   Population: All

   Allele: REF:C ALT:A

   Frequency: C|C:0/026(66) A|A:0/740(1854) A|C:0/233(584)

   Associated Gene: A

   Consequence: Intron Variant

   Clinical Significance: –

   Associated Phenotype / Disease: –

   Information Source: ensembl

   Access Date: 8/4/2026

   پاسخ

5. rsID:
   rs7412

   Chromosome:
   19

   Position (GRCh38):

   Alleles:
   C/T

   Minor Allele:
   50%

   Global Allele Frequency / MAF:
   0.17

   Highest Population Frequency:

   Population:

   Allele:

   Frequency:

   Associated Gene:
   موش

   Consequence:

   Clinical Significance:
   rsID:

   Chromosome:

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   Information Source:

   Access Date:rsID:

   Chromosome:

   Position (GRCh38):

   Alleles:

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   Of the 1,091 plasma metabolites tested, 850 had known identities across eight super pathways (i.e., lipid, amino acid, xenobiotics, nucleotide, cofactor and vitamins, carbohydrate, peptide, and energy). The remaining 241 were categorized as unknown or “partially” characterized molecules. The current study included 81 metabolites that were not tested in previous representative large metabolomics GWASs5,8,10,11,21, although these metabolites may include previously unnamed metabolites. Detailed cohort characteristics can be found in the published CLSA cohort profile23 and Supplementary Table 1, while metabolite information and their comparison with prior large-scale metabolomics GWAS is shown in Supplementary Tables 2, 3 and 4.

   Undertaking a GWAS of metabolite levels identified 1,509 associations for 647 metabolites that passed a stringent Bonferroni correction, adjusted for the total number of tested metabolites (p < 5×10-8/1091 = 4.58×10-11). These included 85 associations for 46 metabolites that were tested uniquely in the current study. Associations passing this stringent Bonferroni correction were used to assess for novel findings (Supplementary Table 5). However, we note that such a multiple-testing correction is overly conservative, given the non-independence of the metabolites (Supplementary Figure 1 and Table 6). We therefore chose to use a more appropriate p-value threshold of 5×10-8 divided by the effective number of independent metabolites (N = 73), leading to a p-value threshold of 6.85×10-10 for subsequent analyses. This relaxed threshold identified 1,702 independent variant-metabolite associations from 690 metabolites that were used to explore the genetic architecture
   of metabolites and identify effector genes. (for details see Methods, Figure 1, Supplementary Table 5). No sign of excessive test statistic inflation or population stratification was detected by assessment of genomic inflation factors (max lambda=1.03) (Supplementary Table 7).

   Associated Phenotype / Disease:
   انیل استارونیل-هیدروکسی ویتامینD-سطوح فسفوپروتیین-پیری-سطوح الانین

   Information Source:
   ensembi pmid-37963177
   Access Date:
   Tue4August

   پاسخ

   1. اصلاحیه پاسخ شما:

      VARIANT 1
      Position (GRCh38): 19:44908822
      Minor Allele: T
      Global Allele Frequency / MAF: T 0.08 (8%)C: 0.92 (92%)
      Highest Population Frequency: 17%
      Associated Gene: APOE
      Consequence: missense_variant

      پاسخ

6. rsID:
   rs429358

   Chromosome:
   19

   Position (GRCh38):

   Alleles:
   T/C
   Minor Allele: C

   Global Allele Frequency / MAF:
   0.62

   Highest Population Frequency:

   Population:1

   Allele:

   Frequency:

   Associated Gene:
   1114ژن مرتبت
   Consequence:

   Clinical Significance: بیماری زا-خطرقطعی وثابت شده

   Associate Phenotype / Disease: الزایمر

   Information Source:
   mim107741

   Access Date:

   پاسخ

   1. اصلاحیه پاسخ شما:

      VARIANT 1
      Position (GRCh38): 19:44908822
      Minor Allele: T
      Global Allele Frequency / MAF: T 0.08 (8%)C: 0.92 (92%)
      Highest Population Frequency: 17%
      Associated Gene: APOE
      Consequence: missense_variant

      پاسخ