# Codebook — Dataset B: 1000 Genomes Exercise and Physiology Gene Variants

This codebook describes only the variables included in the Assignment 4 data files. **n** is the number of people with a value; blank cells in the CSV are missing.

**Files:**
- `genomes_1000g_individuals.csv` (2,504 rows × 44 columns; one row per person)
- `genomes_1000g_population_frequencies.csv` (1,093 rows; one row per variant × population × allele)

**Source:** 1000 Genomes Project, phase 3, via the Ensembl REST API (GRCh38). Open access. https://www.internationalgenome.org/ and https://rest.ensembl.org/

**What it is:** Whole-genome data from 2,504 people in 26 populations on five continents. This file keeps 18 single-letter DNA variants (SNPs) in genes studied in exercise science, physiology and health.

**Notes**
- Everyone has two copies of each gene, one from each parent, so each genotype has two alleles, such as `C/T`. Alleles are written on the forward strand of the genome, sorted alphabetically.
- Each `_count` column gives how many copies of the **counted allele** the person carries (0, 1 or 2).
- These variants have small effects. Associations with performance or health come from studies of groups and do not predict any one person's ability.
- The 1000 Genomes participants have no fitness or health measurements, so these data show how variants differ across people and populations, not their effects.
- In the frequency file, an allele that no one in a population carries is left out rather than listed as 0.

## People

| Variable | Description | Values | n |
|---|---|---|---|
| `sample_id` | 1000 Genomes sample ID |  | 2,504 |
| `sex` | Sex | Male, Female | 2,504 |
| `population` | Population code (26 populations, see table below) | e.g., YRI, CEU, JPT | 2,504 |
| `population_name` | Population name |  | 2,504 |
| `superpopulation` | Continental group code | AFR, AMR, EAS, EUR, SAS | 2,504 |
| `superpopulation_name` | Continental group | African, Admixed American, East Asian, European, South Asian | 2,504 |

## Gene variants

Each variant has two columns: the genotype (for example `actn3_r577x`, values like `C/T`) and the count of the counted allele (for example `actn3_r577x_count`, values 0, 1 or 2).

| Variable | rsID | Gene | Counted allele | What it is | Genotypes in file |
|---|---|---|---|---|---|
| `actn3_r577x`, `actn3_r577x_count` | rs1815739 | *ACTN3* | T | R577X: the T allele stops the protein (577X). XX people make no alpha-actinin-3 in fast-twitch muscle fibers; studied for sprint and power performance | C/C (956), C/T (1089), T/T (459) |
| `ppargc1a_gly482ser`, `ppargc1a_gly482ser_count` | rs8192678 | *PPARGC1A* | T | Gly482Ser in PGC-1α, a regulator of mitochondrial biogenesis; studied for endurance and aerobic training response | C/C (1422), C/T (833), T/T (249) |
| `ampd1_q12x`, `ampd1_q12x_count` | rs17602729 | *AMPD1* | A | Q12X: the A allele stops muscle AMP deaminase; associated with early muscle fatigue and cramps during exercise | A/A (8), A/G (175), G/G (2321) |
| `adrb2_gly16arg`, `adrb2_gly16arg_count` | rs1042713 | *ADRB2* | A | Gly16Arg in the β2-adrenergic receptor (adrenaline response, airway and blood vessel dilation) | A/A (582), A/G (1218), G/G (704) |
| `hif1a_pro582ser`, `hif1a_pro582ser_count` | rs11549465 | *HIF1A* | T | Pro582Ser in HIF-1α, the main oxygen-sensing protein; studied for altitude and anaerobic performance | C/C (2162), C/T (318), T/T (24) |
| `slc16a1_asp490glu`, `slc16a1_asp490glu_count` | rs1049434 | *SLC16A1* | T | Asp490Glu in MCT1, which moves lactate out of muscle; studied for lactate clearance | A/A (331), A/T (957), T/T (1216) |
| `col5a1_rs12722`, `col5a1_rs12722_count` | rs12722 | *COL5A1* | T | Type V collagen (tendons and ligaments); the T allele has been linked to tendon and ligament injury | C/C (1148), C/T (962), T/T (394) |
| `agt_met235thr`, `agt_met235thr_count` | rs699 | *AGT* | G | Met235Thr in angiotensinogen; associated with blood pressure | A/A (315), A/G (847), G/G (1342) |
| `sod2_val16ala`, `sod2_val16ala_count` | rs4880 | *SOD2* | G | Val16Ala in mitochondrial superoxide dismutase (antioxidant defense during exercise) | A/A (935), A/G (1081), G/G (488) |
| `vdr_foki`, `vdr_foki_count` | rs2228570 | *VDR* | G | FokI variant of the vitamin D receptor; the G allele removes the first start codon (shorter receptor). Studied for bone density | A/A (312), A/G (1021), G/G (1171) |
| `bdnf_val66met`, `bdnf_val66met_count` | rs6265 | *BDNF* | T | Val66Met in brain-derived neurotrophic factor; associated with motor learning and memory | C/C (1669), C/T (662), T/T (173) |
| `comt_val158met`, `comt_val158met_count` | rs4680 | *COMT* | A | Val158Met in COMT, which breaks down dopamine in the prefrontal cortex; studied for cognition and pain | A/A (379), A/G (1091), G/G (1034) |
| `fto_rs9939609`, `fto_rs9939609_count` | rs9939609 | *FTO* | A | The best-known obesity-risk variant; each A allele is linked to higher BMI, an effect reduced by physical activity | A/A (343), A/T (1017), T/T (1144) |
| `lct_13910`, `lct_13910_count` | rs4988235 | *LCT/MCM6* | A | The A allele keeps lactase active into adulthood (can digest milk) | A/A (197), A/G (414), G/G (1893) |
| `cyp1a2_163c_a`, `cyp1a2_163c_a_count` | rs762551 | *CYP1A2* | A | CYP1A2*1F: the A allele is linked to faster caffeine metabolism; studied for caffeine's effect on performance | A/A (1031), A/C (1092), C/C (381) |
| `slc24a5_ala111thr`, `slc24a5_ala111thr_count` | rs1426654 | *SLC24A5* | A | Ala111Thr: the A allele is linked to lighter skin, which affects vitamin D synthesis | A/A (892), A/G (408), G/G (1204) |
| `apoe_rs429358`, `apoe_rs429358_count` | rs429358 | *APOE* | C | One of the two variants that define APOE ε2/ε3/ε4; the C allele marks ε4 | C/C (71), C/T (612), T/T (1821) |
| `apoe_rs7412`, `apoe_rs7412_count` | rs7412 | *APOE* | T | The other APOE variant; the T allele marks ε2 | C/C (2142), C/T (348), T/T (14) |
| `apoe_genotype` | rs429358 + rs7412 | *APOE* | — | APOE type built from the two APOE variants (ε2, ε3 or ε4 from each parent). ε4 is the strongest common genetic risk factor for Alzheimer's disease | e3/e3 (1525), e3/e4 (547), e2/e3 (282), e4/e4 (70), e2/e4 (65), e2/e2 (14) |
| `apoe_e4_count` | rs429358 | *APOE* | C | Number of ε4 copies (0, 1 or 2) | — |

## Population frequencies file

| Variable | Description | Values |
|---|---|---|
| `variant` | Variant name, matching the column names above | e.g., `actn3_r577x` |
| `rsid` | dbSNP ID | e.g., rs1815739 |
| `gene` | Gene | e.g., ACTN3 |
| `population` | Population or continental group code | 26 populations + AFR, AMR, EAS, EUR, SAS |
| `population_name` | Full name | |
| `level` | Whether the row is one population or a continental group | population, superpopulation |
| `allele` | DNA letter (forward strand) | A, C, G, T |
| `is_counted_allele` | Whether this is the counted allele from the table above | True, False |
| `allele_meaning` | What the counted allele is (blank for the other allele) | |
| `frequency` | Share of all copies in that population that carry this allele | 0 to 1 |
| `allele_count` | Number of copies carrying this allele | count |

## Populations

| Code | Population | Continental group | People |
|---|---|---|---|
| ACB | African Caribbean in Barbados | AFR | 96 |
| ASW | African Ancestry in Southwest US | AFR | 61 |
| BEB | Bengali in Bangladesh | SAS | 86 |
| CDX | Chinese Dai in Xishuangbanna, China | EAS | 93 |
| CEU | Utah residents with Northern and Western European ancestry | EUR | 99 |
| CHB | Han Chinese in Beijing, China | EAS | 103 |
| CHS | Southern Han Chinese | EAS | 105 |
| CLM | Colombian in Medellin, Colombia | AMR | 94 |
| ESN | Esan in Nigeria | AFR | 99 |
| FIN | Finnish in Finland | EUR | 99 |
| GBR | British in England and Scotland | EUR | 91 |
| GIH | Gujarati Indian in Houston, TX | SAS | 103 |
| GWD | Gambian in Western Division, The Gambia | AFR | 113 |
| IBS | Iberian populations in Spain | EUR | 107 |
| ITU | Indian Telugu in the UK | SAS | 102 |
| JPT | Japanese in Tokyo, Japan | EAS | 104 |
| KHV | Kinh in Ho Chi Minh City, Vietnam | EAS | 99 |
| LWK | Luhya in Webuye, Kenya | AFR | 99 |
| MSL | Mende in Sierra Leone | AFR | 85 |
| MXL | Mexican Ancestry in Los Angeles, CA | AMR | 64 |
| PEL | Peruvian in Lima, Peru | AMR | 85 |
| PJL | Punjabi in Lahore, Pakistan | SAS | 96 |
| PUR | Puerto Rican in Puerto Rico | AMR | 104 |
| STU | Sri Lankan Tamil in the UK | SAS | 102 |
| TSI | Toscani in Italy | EUR | 107 |
| YRI | Yoruba in Ibadan, Nigeria | AFR | 108 |