import os
import re
import numpy as np
import pandas as pd
import pickle
import matplotlib.pyplot as plt
from adjustText import adjust_text
import textalloc
from pymir import mpl_stylesheet
from pymir import mpl_utils
mpl_stylesheet.banskt_presentation(splinecolor = 'black', dpi = 120, colors = 'kelly')
from matplotlib.gridspec import GridSpec
import sys
sys.path.append("../utils/")
import simulate as mpy_simulatedata_dir = "/gpfs/commons/home/sbanerjee/work/npd/PanUKB/data"
result_dir = "/gpfs/commons/home/sbanerjee/work/npd/PanUKB/results/nnsparsh/noRx"
# h2_cut = 0.1
# pval_cut = 5e-8
zscore_df = pd.read_pickle(os.path.join(data_dir, f"modselect/zscore_noRx.pkl"))
# trait_df = pd.read_pickle(os.path.join(data_dir, f"modselect/traits_noRx.pkl"))
trait_df = pd.read_pickle(os.path.join(data_dir, f"modselect/traits_all_with_desc.pkl"))
variant_filename = f"{data_dir}/allvar.pruned.closesttss.hugo"
variant_df = pd.read_csv(variant_filename, sep = '\t')# def compute_cos(xmat):
# xstd = xmat / np.sqrt(np.var(xmat, axis = 1, keepdims = True))
# xstd2 = xstd ** 2
# return xstd2 / np.sum(xstd2, axis = 1, keepdims = True)
# def compute_contribution(xmat):
# xstd = xmat / np.sqrt(np.var(xmat, axis = 0, keepdims = True))
# xstd2 = xstd ** 2
# return xstd2 / np.sum(xstd2, axis = 0, keepdims = True)
# def compute_contribution(factor):
# return (factor ** 2) / (np.sum(factor ** 2, axis = 0).reshape((1, factor.shape[1])))
# def compute_cos(factor):
# return (factor ** 2) / (np.sum(factor ** 2, axis = 1).reshape((factor.shape[0], 1)))
def get_principal_components(X):
X_cent = mpy_simulate.do_standardize(X, scale = False)
X_cent /= np.sqrt(np.prod(X_cent.shape))
U, S, Vt = np.linalg.svd(X_cent, full_matrices = False)
loadings = U @ np.diag(S)
factors = Vt.T
return U, S, loadings, factors
def compute_cos(xmat):
xmat2 = xmat ** 2
return xmat2 / np.sum(xmat2, axis = 1, keepdims = True)
def compute_contribution(xmat):
xmat2 = xmat ** 2
return xmat2 / np.sum(xmat2, axis = 0, keepdims = True)method = 'rpca'
res_filename = os.path.join(result_dir, f"{method}_model.pkl")
with (open(res_filename, "rb")) as fh:
lowrank_model = pickle.load(fh)lowrank_model.keys()dict_keys(['rho_', 'max_iter_', 'mu_update_method_', 'tau_', 'primal_tol_', 'dual_tol_', 'prog_step_skip_', 'show_progress_', 'is_debug_', 'is_benchmark_', 'benchmark_method_', 'mask_', 'mu_list_', 'primal_res_', 'dual_res_', 'cpu_time_', 'L_', 'E_'])U, S, loadings, factors = get_principal_components(lowrank_model['L_'])
cos2_pheno = compute_cos(loadings)
cos2_variant = compute_cos(factors)
contribution_pheno = compute_contribution(loadings)
contribution_variant = compute_contribution(factors)
# cos2_pheno = get_cos2_scores(loadings)
# contribution_pheno = get_contribution_scores(loadings)pheno_zindex = [int(x[1:]) for x in zscore_df.columns]
trait_df_noRx = trait_df.loc[trait_df['zindex'].isin(pheno_zindex)]
trait_df_noRx.info()<class 'pandas.core.frame.DataFrame'>
Index: 2110 entries, 0 to 2482
Data columns (total 20 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 zindex 2110 non-null int64
1 trait_type 2110 non-null object
2 phenocode 2110 non-null object
3 pheno_sex 2110 non-null object
4 coding 267 non-null object
5 modifier 394 non-null object
6 description 2110 non-null object
7 description_more 1408 non-null object
8 coding_description 261 non-null object
9 category 2072 non-null object
10 BIN_QT 2110 non-null object
11 n_cases_EUR 2110 non-null int64
12 n_controls_EUR 1304 non-null float64
13 N 2110 non-null int64
14 Neff 2110 non-null float64
15 filename 2110 non-null object
16 aws_link 2110 non-null object
17 estimates.final.h2_observed 2106 non-null float64
18 long_description 2110 non-null object
19 short_description 2110 non-null object
dtypes: float64(3), int64(3), object(14)
memory usage: 346.2+ KBtrait_df_noRx['description'].to_list()['A04 Other bacterial intestinal infections',
'A08 Viral and other specified intestinal infections',
'A09 Diarrhoea and gastro-enteritis of presumed infectious origin',
'A41 Other septicaemia',
'B34 Viral infection of unspecified site',
'B37 Candidiasis',
'B95 Streptococcus and staphylococcus as the cause of diseases classified to other chapters',
'B96 Other bacterial agents as the cause of diseases classified to other chapters',
'B98 Other specified infectious agents as the cause of diseases classified to other chapters',
'C18 Malignant neoplasm of colon',
'C34 Malignant neoplasm of bronchus and lung',
'C43 Malignant melanoma of skin',
'C44 Other malignant neoplasms of skin',
'C50 Malignant neoplasm of breast',
'C54 Malignant neoplasm of corpus uteri',
'C67 Malignant neoplasm of bladder',
'C77 Secondary and unspecified malignant neoplasm of lymph nodes',
'C78 Secondary malignant neoplasm of respiratory and digestive organs',
'C79 Secondary malignant neoplasm of other sites',
'C80 Malignant neoplasm without specification of site',
"C83 Diffuse non-Hodgkin's lymphoma",
"C85 Other and unspecified types of non-Hodgkin's lymphoma",
'D05 Carcinoma in situ of breast',
'D12 Benign neoplasm of colon, rectum, anus and anal canal',
'D13 Benign neoplasm of other and ill-defined parts of digestive system',
'D17 Benign lipomatous neoplasm',
'D18 Haemangioma and lymphangioma, any site',
'D22 Melanocytic naevi',
'D23 Other benign neoplasms of skin',
'D25 Leiomyoma of uterus',
'D35 Benign neoplasm of other and unspecified endocrine glands',
'D37 Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs',
'D50 Iron deficiency anaemia',
'D51 Vitamin B12 deficiency anaemia',
'D64 Other anaemias',
'D68 Other coagulation defects',
'D69 Purpura and other haemorrhagic conditions',
'E03 Other hypothyroidism',
'E04 Other non-toxic goitre',
'E05 Thyrotoxicosis [hyperthyroidism]',
'E10 Insulin-dependent diabetes mellitus',
'E11 Non-insulin-dependent diabetes mellitus',
'E14 Unspecified diabetes mellitus',
'E16 Other disorders of pancreatic internal secretion',
'E21 Hyperparathyroidism and other disorders of parathyroid gland',
'E53 Deficiency of other B group vitamins',
'E66 Obesity',
'E78 Disorders of lipoprotein metabolism and other lipidaemias',
'E83 Disorders of mineral metabolism',
'E87 Other disorders of fluid, electrolyte and acid-base balance',
'E89 Postprocedural endocrine and metabolic disorders, not elsewhere classified',
'F05 Delirium, not induced by alcohol and other psychoactive substances',
'F10 Mental and behavioural disorders due to use of alcohol',
'F17 Mental and behavioural disorders due to use of tobacco',
'F31 Bipolar affective disorder',
'F32 Depressive episode',
'F41 Other anxiety disorders',
'G40 Epilepsy',
'G43 Migraine',
'G45 Transient cerebral ischaemic attacks and related syndromes',
'G47 Sleep disorders',
'G51 Facial nerve disorders',
'G55 Nerve root and plexus compressions in diseases classified elsewhere',
'G56 Mononeuropathies of upper limb',
'G57 Mononeuropathies of lower limb',
'G62 Other polyneuropathies',
'G81 Hemiplegia',
'G93 Other disorders of brain',
'G99 Other disorders of nervous system in diseases classified elsewhere',
'H00 Hordeolum and chalazion',
'H02 Other disorders of eyelid',
'H04 Disorders of lachrymal system',
'H25 Senile cataract',
'H26 Other cataract',
'H33 Retinal detachments and breaks',
'H35 Other retinal disorders',
'H36 Retinal disorders in diseases classified elsewhere',
'H40 Glaucoma',
'H43 Disorders of vitreous body',
'H50 Other strabismus',
'H52 Disorders of refraction and accommodation',
'H53 Visual disturbances',
'H54 Blindness and low vision',
'H61 Other disorders of external ear',
'H65 Nonsuppurative otitis media',
'H72 Perforation of tympanic membrane',
'H81 Disorders of vestibular function',
'H90 Conductive and sensorineural hearing loss',
'H91 Other hearing loss',
'I08 Multiple valve diseases',
'I12 Hypertensive renal disease',
'I20 Angina pectoris',
'I21 Acute myocardial infarction',
'I24 Other acute ischaemic heart diseases',
'I25 Chronic ischaemic heart disease',
'I26 Pulmonary embolism',
'I27 Other pulmonary heart diseases',
'I31 Other diseases of pericardium',
'I34 Nonrheumatic mitral valve disorders',
'I35 Nonrheumatic aortic valve disorders',
'I42 Cardiomyopathy',
'I44 Atrioventricular and left bundle-branch block',
'I45 Other conduction disorders',
'I46 Cardiac arrest',
'I47 Paroxysmal tachycardia',
'I48 Atrial fibrillation and flutter',
'I49 Other cardiac arrhythmias',
'I50 Heart failure',
'I51 Complications and ill-defined descriptions of heart disease',
'I61 Intracerebral haemorrhage',
'I63 Cerebral infarction',
'I65 Occlusion and stenosis of precerebral arteries, not resulting in cerebral infarction',
'I67 Other cerebrovascular diseases',
'I69 Sequelae of cerebrovascular disease',
'I71 Aortic aneurysm and dissection',
'I73 Other peripheral vascular diseases',
'I74 Arterial embolism and thrombosis',
'I77 Other disorders of arteries and arterioles',
'I80 Phlebitis and thrombophlebitis',
'I83 Varicose veins of lower extremities',
'I84 Haemorrhoids',
'I95 Hypotension',
'J02 Acute pharyngitis',
'J18 Pneumonia, organism unspecified',
'J30 Vasomotor and allergic rhinitis',
'J31 Chronic rhinitis, nasopharyngitis and pharyngitis',
'J32 Chronic sinusitis',
'J33 Nasal polyp',
'J34 Other disorders of nose and nasal sinuses',
'J35 Chronic diseases of tonsils and adenoids',
'J38 Diseases of vocal cords and larynx, not elsewhere classified',
'J43 Emphysema',
'J44 Other chronic obstructive pulmonary disease',
'J45 Asthma',
'J84 Other interstitial pulmonary diseases',
'J92 Pleural plaque',
'J93 Pneumothorax',
'J96 Respiratory failure, not elsewhere classified',
'J98 Other respiratory disorders',
'K01 Embedded and impacted teeth',
'K02 Dental caries',
'K04 Diseases of pulp and periapical tissues',
'K08 Other disorders of teeth and supporting structures',
'K11 Diseases of salivary glands',
'K12 Stomatitis and related lesions',
'K13 Other diseases of lip and oral mucosa',
'K14 Diseases of tongue',
'K21 Gastro-oesophageal reflux disease',
'K22 Other diseases of oesophagus',
'K25 Gastric ulcer',
'K26 Duodenal ulcer',
'K29 Gastritis and duodenitis',
'K31 Other diseases of stomach and duodenum',
'K35 Acute appendicitis',
'K40 Inguinal hernia',
'K42 Umbilical hernia',
'K43 Ventral hernia',
'K44 Diaphragmatic hernia',
"K50 Crohn's disease [regional enteritis]",
'K51 Ulcerative colitis',
'K52 Other non-infective gastro-enteritis and colitis',
'K55 Vascular disorders of intestine',
'K56 Paralytic ileus and intestinal obstruction without hernia',
'K57 Diverticular disease of intestine',
'K58 Irritable bowel syndrome',
'K59 Other functional intestinal disorders',
'K60 Fissure and fistula of anal and rectal regions',
'K61 Abscess of anal and rectal regions',
'K62 Other diseases of anus and rectum',
'K63 Other diseases of intestine',
'K64 Haemorrhoids and perianal venous thrombosis',
'K65 Peritonitis',
'K66 Other disorders of peritoneum',
'K70 Alcoholic liver disease',
'K74 Fibrosis and cirrhosis of liver',
'K76 Other diseases of liver',
'K80 Cholelithiasis',
'K81 Cholecystitis',
'K82 Other diseases of gallbladder',
'K83 Other diseases of biliary tract',
'K85 Acute pancreatitis',
'K86 Other diseases of pancreas',
'K90 Intestinal malabsorption',
'K91 Postprocedural disorders of digestive system, not elsewhere classified',
'K92 Other diseases of digestive system',
'L02 Cutaneous abscess, furuncle and carbuncle',
'L03 Cellulitis',
'L08 Other local infections of skin and subcutaneous tissue',
'L30 Other dermatitis',
'L40 Psoriasis',
'L57 Skin changes due to chronic exposure to nonionising radiation',
'L60 Nail disorders',
'L72 Follicular cysts of skin and subcutaneous tissue',
'L89 Decubitus ulcer',
'L90 Atrophic disorders of skin',
'L91 Hypertrophic disorders of skin',
'L98 Other disorders of skin and subcutaneous tissue, not elsewhere classified',
'M06 Other rheumatoid arthritis',
'M10 Gout',
'M13 Other arthritis',
'M15 Polyarthrosis',
'M16 Coxarthrosis [arthrosis of hip]',
'M17 Gonarthrosis [arthrosis of knee]',
'M18 Arthrosis of first carpometacarpal joint',
'M19 Other arthrosis',
'M20 Acquired deformities of fingers and toes',
'M22 Disorders of patella',
'M23 Internal derangement of knee',
'M25 Other joint disorders, not elsewhere classified',
'M35 Other systemic involvement of connective tissue',
'M47 Spondylosis',
'M48 Other spondylopathies',
'M50 Cervical disk disorders',
'M51 Other intervertebral disk disorders',
'M54 Dorsalgia',
'M65 Synovitis and tenosynovitis',
'M67 Other disorders of synovium and tendon',
'M70 Soft tissue disorders related to use, overuse and pressure',
'M72 Fibroblastic disorders',
'M75 Shoulder lesions',
'M77 Other enthesopathies',
'M79 Other soft tissue disorders, not elsewhere classified',
'M81 Osteoporosis without pathological fracture',
'N13 Obstructive and reflux uropathy',
'N17 Acute renal failure',
'N18 Chronic renal failure',
'N20 Calculus of kidney and ureter',
'N28 Other disorders of kidney and ureter, not elsewhere classified',
'N30 Cystitis',
'N31 Neuromuscular dysfunction of bladder, not elsewhere classified',
'N32 Other disorders of bladder',
'N35 Urethral stricture',
'N39 Other disorders of urinary system',
'N41 Inflammatory diseases of prostate',
'N42 Other disorders of prostate',
'N43 Hydrocele and spermatocele',
'N48 Other disorders of penis',
'N50 Other disorders of male genital organs',
'N60 Benign mammary dysplasia',
'N64 Other disorders of breast',
'N73 Other female pelvic inflammatory diseases',
'N80 Endometriosis',
'N81 Female genital prolapse',
'N83 Noninflammatory disorders of ovary, Fallopian tube and broad ligament',
'N84 Polyp of female genital tract',
'N85 Other noninflammatory disorders of uterus, except cervix',
'N87 Dysplasia of cervix uteri',
'N88 Other noninflammatory disorders of cervix uteri',
'N89 Other noninflammatory disorders of vagina',
'N90 Other noninflammatory disorders of vulva and perineum',
'N92 Excessive, frequent and irregular menstruation',
'N93 Other abnormal uterine and vaginal bleeding',
'N94 Pain and other conditions associated with female genital organs and menstrual cycle',
'N95 Menopausal and other perimenopausal disorders',
'N99 Postprocedural disorders of genito-urinary system, not elsewhere classified',
'O02 Other abnormal products of conception',
'O03 Spontaneous abortion',
'O04 Medical abortion',
'O26 Maternal care for other conditions predominantly related to pregnancy',
'O32 Maternal care for known or suspected malpresentation of foetus',
'O34 Maternal care for known or suspected abnormality of pelvic organs',
'O36 Maternal care for other known or suspected foetal problems',
'O42 Premature rupture of membranes',
'O47 False labour',
'O63 Long labour',
'O68 Labour and delivery complicated by foetal stress [distress]',
'O70 Perineal laceration during delivery',
'O72 Postpartum haemorrhage',
'O80 Single spontaneous delivery',
'O99 Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium',
'R00 Abnormalities of heart beat',
'R01 Cardiac murmurs and other cardiac sounds',
'R03 Abnormal blood-pressure reading, without diagnosis',
'R04 Haemorrhage from respiratory passages',
'R06 Abnormalities of breathing',
'R07 Pain in throat and chest',
'R09 Other symptoms and signs involving the circulatory and respiratory systems',
'R10 Abdominal and pelvic pain',
'R19 Other symptoms and signs involving the digestive system and abdomen',
'R20 Disturbances of skin sensation',
'R22 Localised swelling, mass and lump of skin and subcutaneous tissue',
'R25 Abnormal involuntary movements',
'R26 Abnormalities of gait and mobility',
'R29 Other symptoms and signs involving the nervous and musculoskeletal systems',
'R30 Pain associated with micturition',
'R39 Other symptoms and signs involving the urinary system',
'R41 Other symptoms and signs involving cognitive functions and awareness',
'R45 Symptoms and signs involving emotional state',
'R47 Speech disturbances, not elsewhere classified',
'R49 Voice disturbances',
'R50 Fever of unknown origin',
'R52 Pain, not elsewhere classified',
'R56 Convulsions, not elsewhere classified',
'R59 Enlarged lymph nodes',
'R60 Oedema, not elsewhere classified',
'R63 Symptoms and signs concerning food and fluid intake',
'R79 Other abnormal findings of blood chemistry',
'R87 Abnormal findings in specimens from female genital organs',
'R93 Abnormal findings on diagnostic imaging of other body structures',
'S00 Superficial injury of head',
'S01 Open wound of head',
'S09 Other and unspecified injuries of head',
'S61 Open wound of wrist and hand',
'S66 Injury of muscle and tendon at wrist and hand level',
'S80 Superficial injury of lower leg',
'S82 Fracture of lower leg, including ankle',
'T39 Poisoning by nonopioid analgesics, antipyretics and antirheumatics',
'T42 Poisoning by antiepileptic, sedative-hypnotic and anti-Parkinsonism drugs',
'T43 Poisoning by psychotropic drugs, not elsewhere classified',
'T51 Toxic effect of alcohol',
'T78 Adverse effects, not elsewhere classified',
'T81 Complications of procedures, not elsewhere classified',
'T82 Complications of cardiac and vascular prosthetic devices, implants and grafts',
'T83 Complications of genito-urinary prosthetic devices, implants and grafts',
'T84 Complications of internal orthopaedic prosthetic devices, implants and grafts',
'T85 Complications of other internal prosthetic devices, implants and grafts',
'V18 Pedal cyclist injured in noncollision transport accident',
'W00 Fall on same level involving ice and snow',
'W01 Fall on same level from slipping, tripping and stumbling',
'W10 Fall on and from stairs and steps',
'W11 Fall on and from ladder',
'W18 Other fall on same level',
'W19 Unspecified fall',
'X50 Overexertion and strenuous or repetitive movements',
'X59 Exposure to unspecified factor',
'X60 Intentional self-poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics',
'X61 Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, anti-Parkinsonism and psychotropic drugs, not elsewhere classified',
'Y42 Hormones and their synthetic substitutes and antagonists, not elsewhere classified',
'Y43 Primarily systemic agents',
'Y45 Analgesics, antipyretics and anti-inflammatory drugs',
'Y83 Surgical operation and other surgical procedures as the cause of abnormal reaction of the patient, or of later complication, without mention of misadventure at the time of the procedure',
'Y84 Other medical procedures as the cause of abnormal reaction of the patient, or of later complication, without mention of misadventure at the time of the procedure',
'Z01 Other special examinations and investigations of persons without complaint or reported diagnosis',
'Z02 Examination and encounter for administrative purposes',
'Z03 Medical observation and evaluation for suspected diseases and conditions',
'Z04 Examination and observation for other reasons',
'Z08 Follow-up examination after treatment for malignant neoplasm',
'Z09 Follow-up examination after treatment for conditions other than malignant neoplasms',
'Z12 Special screening examination for neoplasms',
'Z13 Special screening examination for other diseases and disorders',
'Z22 Carrier of infectious disease',
'Z30 Contraceptive management',
'Z34 Supervision of normal pregnancy',
'Z35 Supervision of high-risk pregnancy',
'Z36 Antenatal screening',
'Z42 Follow-up care involving plastic surgery',
'Z43 Attention to artificial openings',
'Z45 Adjustment and management of implanted device',
'Z46 Fitting and adjustment of other devices',
'Z47 Other orthopaedic follow-up care',
'Z48 Other surgical follow-up care',
'Z50 Care involving use of rehabilitation procedures',
'Z51 Other medical care',
'Z53 Persons encountering health services for specifie procedures, not carried out',
'Z60 Problems related to social environment',
'Z71 Persons encountering health services for other counselling and medical advice, not elsewhere classified',
'Z72 Problems related to lifestyle',
'Z75 Problems related to medical facilities and other health care',
'Z80 Family history of malignant neoplasm',
'Z82 Family history of certain disabilities and chronic diseases leading to disablement',
'Z83 Family history of other specific disorders',
'Z85 Personal history of malignant neoplasm',
'Z86 Personal history of certain other diseases',
'Z87 Personal history of other diseases and conditions',
'Z88 Personal history of allergy to drugs, medicaments and biologocal substances',
'Z90 Acquired absence of organs, not elsewhere classified',
'Z91 Personal history of risk-factors, not elsewhere classified',
'Z92 Personal history of medical treatment',
'Z93 Artificial opening status',
'Z94 Transplanted organ and tissue status',
'Z95 Presence of cardiac and vascular implants and grafts',
'Z96 Presence of other functional implants',
'Z97 Presence of other devices',
'Z98 Other postsurgical states',
'Z99 Dependence on enabling machines and devices, not elsewhere classified',
'Intestinal infection',
'Bacterial enteritis',
'Viral Enteritis',
'Septicemia',
'Gram negative septicemia',
'Bacterial infection NOS',
'Staphylococcus infections',
'Streptococcus infection',
'E. coli',
'Viral warts & HPV',
'Viral infection',
'Postoperative infection',
'Infection/inflammation of internal prosthetic device; implant; and graft',
'Foreign body injury',
'Symptoms concerning nutrition, metabolism, and development',
'Other symptoms',
'Crushing or internal injury to organs',
'Injury, NOS',
'Other tests',
'Complications of surgical and medical procedures',
'Effects of other external causes',
'Other ill-defined and unknown causes of morbidity and mortality',
'Family history',
'Candidiasis',
'Colorectal cancer',
'Colon cancer',
'Malignant neoplasm of rectum, rectosigmoid junction, and anus',
'Neoplasm of unspecified nature of digestive system',
'Malignant neoplasm of other and ill-defined sites within the digestive organs and peritoneum',
'Cancer within the respiratory system',
'Cancer of bronchus; lung',
'Skin cancer',
'Melanomas of skin, dx or hx',
'Other non-epithelial cancer of skin',
'Breast cancer',
'Breast cancer [female]',
'Malignant neoplasm of female breast',
'Acquired absence of breast',
'Cervical cancer and dysplasia',
'Cervical intraepithelial neoplasia [CIN] [Cervical dysplasia]',
'Malignant neoplasm of uterus',
'Cancer of other female genital organs',
'Malignant neoplasm of ovary and other uterine adnexa',
'Malignant neoplasm of ovary',
'Cancer of prostate',
'Cancer of urinary organs (incl. kidney and bladder)',
'Cancer of kidney and renal pelvis',
'Malignant neoplasm of kidney, except pelvis',
'Cancer of bladder',
'Malignant neoplasm of bladder',
'Cancer, suspected or other',
'Malignant neoplasm, other',
'Chemotherapy',
'Secondary malignant neoplasm',
'Secondary malignancy of lymph nodes',
'Secondary malignancy of respiratory organs',
'Secondary malignant neoplasm of digestive systems',
'Secondary malignant neoplasm of liver',
'Secondary malignancy of brain/spine',
'Secondary malignancy of bone',
'Neoplasm of uncertain behavior',
'Myeloproliferative disease',
'Cancer of other lymphoid, histiocytic tissue',
'Non-Hodgkins lymphoma',
'Leukemia',
'Benign neoplasm of colon',
'Benign neoplasm of lip, oral cavity, and pharynx',
'Benign neoplasm of other parts of digestive system',
'Lipoma',
'Lipoma of skin and subcutaneous tissue',
'Other benign neoplasm of connective and other soft tissue',
'Benign neoplasm of skin',
'Benign neoplasm of uterus',
'Uterine leiomyoma',
'Benign neoplasm of ovary',
'Benign neoplasm of other endocrine glands and related structures',
'Hemangioma and lymphangioma, any site',
'Nontoxic nodular goiter',
'Thyrotoxicosis with or without goiter',
'Hypothyroidism',
'Secondary hypothyroidism',
'Hypothyroidism NOS',
'Diabetes mellitus',
'Type 1 diabetes',
'Type 2 diabetes',
'Type 2 diabetes with ophthalmic manifestations',
'Diabetic retinopathy',
'Other disorders of pancreatic internal secretion',
'Hypoglycemia',
'Disorders of parathyroid gland',
'Hyperparathyroidism',
'Anorexia',
'Vitamin deficiency',
'Vitamin B-complex deficiencies',
'Vitamin D deficiency',
'Disorders of lipoid metabolism',
'Hyperlipidemia',
'Hypercholesterolemia',
'Gout and other crystal arthropathies',
'Gout',
'Disorders of mineral metabolism',
'Disorders of calcium/phosphorus metabolism',
'Disorders of fluid, electrolyte, and acid-base balance',
'Electrolyte imbalance',
'Hyposmolality and/or hyponatremia',
'Hyperpotassemia',
'Hypopotassemia',
'Acid-base balance disorder',
'Acidosis',
'Hypovolemia',
'Other disorders of metabolism',
'Overweight, obesity and other hyperalimentation',
'Obesity',
'Iron deficiency anemias',
'Iron deficiency anemias, unspecified or not due to blood loss',
'Other deficiency anemia',
'Megaloblastic anemia',
'Other vitamin B12 deficiency anemia',
'Other anemias',
'Coagulation defects',
'Defibrination syndrome',
'Purpura and other hemorrhagic conditions',
'Thrombocytopenia',
'Diseases of white blood cells',
'Decreased white blood cell count',
'Other diseases of blood and blood-forming organs',
'Lymphadenitis',
'Delirium dementia and amnestic and other cognitive disorders',
'Dementias',
'Delirium due to conditions classified elsewhere',
'Other specified nonpsychotic and/or transient mental disorders',
'Neurological disorders',
'Aphasia/speech disturbance',
'Altered mental status',
'Symptoms involving head and neck',
'Swelling, mass, or lump in head and neck [Space-occupying lesion, intracranial NOS]',
'Schizophrenia and other psychotic disorders',
'Mood disorders',
'Bipolar',
'Suicidal ideation or attempt',
'Suicide or self-inflicted injury',
'Anxiety disorders',
'Anxiety disorder',
'Agorophobia, social phobia, and panic disorder',
'Other mental disorder',
'Substance addiction and disorders',
'Alcohol-related disorders',
'Alcoholism',
'Alcoholic liver damage',
'Tobacco use disorder',
'Sleep disorders',
'Sleep apnea',
'Other cerebral degenerations',
"Parkinson's disease",
'Extrapyramidal disease and abnormal movement disorders',
'Degenerative disease of the spinal cord',
'Multiple sclerosis',
'Other headache syndromes',
'Migraine',
'Hemiplegia',
'Epilepsy, recurrent seizures, convulsions',
'Epilepsy',
'Convulsions',
'Abnormal movement',
'Abnormal involuntary movements',
'Abnormality of gait',
'Other peripheral nerve disorders',
'Disorders of other cranial nerves',
'Facial nerve disorders [CN7]',
'Nerve root and plexus disorders',
'Inflammatory and toxic neuropathy',
'Retinal detachments and defects',
'Retinal detachment with retinal defect',
'Other retinal disorders',
'Degeneration of macula and posterior pole of retina',
'Macular degeneration (senile) of retina NOS',
'Retinal vascular changes and abnomalities',
'Hereditary retinal dystrophies',
'Glaucoma',
'Open-angle glaucoma',
'Primary open angle glaucoma',
'Cataract',
'Senile cataract',
'Disorders of refraction and accommodation; blindness and low vision',
'Myopia',
'Blindness and low vision',
'Visual disturbances',
'Inflammation of the eye',
'Inflammation of eyelids',
'Other disorders of eyelids',
'Ectropion or entropion',
'Ptosis of eyelid',
'Disorders of lacrimal system',
'Epiphora',
'Strabismus and other disorders of binocular eye movements',
'Strabismus (not specified as paralytic)',
'Other disorders of eye',
'Disorders of vitreous body',
'Aphakia and other disorders of lens',
'Disorders of external ear',
'Otitis media and Eustachian tube disorders',
'Otitis media',
'Other disorders of tympanic membrane',
'Perforation of tympanic membrane',
'Vertiginous syndromes and other disorders of vestibular system',
'Dizziness and giddiness (Light-headedness and vertigo)',
'Hearing loss',
'Rheumatic disease of the heart valves',
'Mitral valve disease',
'Aortic valve disease',
'Heart valve disorders',
'Nonrheumatic mitral valve disorders',
'Nonrheumatic aortic valve disorders',
'Heart valve replaced',
'Abnormal heart sounds',
'Hypertension',
'Essential hypertension',
'Hypertensive heart and/or renal disease',
'Hypertensive chronic kidney disease',
'Elevated blood pressure reading without diagnosis of hypertension',
'Ischemic Heart Disease',
'Unstable angina (intermediate coronary syndrome)',
'Myocardial infarction',
'Angina pectoris',
'Coronary atherosclerosis',
'Other chronic ischemic heart disease, unspecified',
'Other acute and subacute forms of ischemic heart disease',
'Other forms of chronic heart disease',
'Pulmonary heart disease',
'Acute pulmonary heart disease',
'Pulmonary embolism and infarction, acute',
'Cardiomegaly',
'Nonspecific chest pain',
'Precordial pain',
'Carditis',
'Pericarditis',
'Cardiomyopathy',
'Primary/intrinsic cardiomyopathies',
'Cardiac conduction disorders',
'Atrioventricular [AV] block',
'First degree AV block',
'Bundle branch block',
'Right bundle branch block',
'Left bundle branch block',
'Cardiac pacemaker/device in situ',
'Cardiac pacemaker in situ',
'Cardiac dysrhythmias',
'Paroxysmal tachycardia, unspecified',
'Paroxysmal supraventricular tachycardia',
'Paroxysmal ventricular tachycardia',
'Atrial fibrillation and flutter',
'Other specified cardiac dysrhythmias',
'Cardiac arrest and ventricular fibrillation',
'Cardiac arrest',
'Arrhythmia (cardiac) NOS',
'Tachycardia NOS',
'Palpitations',
'Congestive heart failure; nonhypertensive',
'Congestive heart failure (CHF) NOS',
'Heart failure NOS',
'Ill-defined descriptions and complications of heart disease',
'Intracranial hemorrhage',
'Subarachnoid hemorrhage',
'Intracerebral hemorrhage',
'Cerebrovascular disease',
'Occlusion and stenosis of precerebral arteries',
'Occlusion of cerebral arteries',
'Cerebral artery occlusion, with cerebral infarction',
'Cerebral ischemia',
'Transient cerebral ischemia',
'Late effects of cerebrovascular disease',
'Atherosclerosis',
'Atherosclerosis of the extremities',
'Vascular insufficiency of intestine',
'Other aneurysm',
'Aortic aneurysm',
'Abdominal aortic aneurysm',
'Peripheral vascular disease',
"Raynaud's syndrome",
'Peripheral vascular disease, unspecified',
'Arterial embolism and thrombosis',
'Polyarteritis nodosa and allied conditions',
'Other disorders of arteries and arterioles',
'Stricture of artery',
'Noninfectious disorders of lymphatic channels',
'Phlebitis and thrombophlebitis',
'Phlebitis and thrombophlebitis of lower extremities',
'Varicose veins',
'Varicose veins of lower extremity',
'Hemorrhoids',
'Hypotension',
'Orthostatic hypotension',
'Hypotension NOS',
'Other disorders of circulatory system',
'Circulatory disease NEC',
'Acute upper respiratory infections of multiple or unspecified sites',
'Acute pharyngitis',
'Septal Deviations/Turbinate Hypertrophy',
'Nasal polyps',
'Chronic pharyngitis and nasopharyngitis',
'Diseases of the larynx and vocal cords',
'Voice disturbance',
'Acute and chronic tonsillitis',
'Chronic tonsillitis and adenoiditis',
'Chronic sinusitis',
'Allergic rhinitis',
'Epistaxis or throat hemorrhage',
'Other upper respiratory disease',
'Pneumonia',
'Bacterial pneumonia',
'Pneumococcal pneumonia',
'Asthma',
'Chronic airway obstruction',
'Emphysema',
'Chronic bronchitis',
'Obstructive chronic bronchitis',
'Bronchiectasis',
'Postinflammatory pulmonary fibrosis',
'Empyema and pneumothorax',
'Pleurisy; pleural effusion',
'Pulmonary collapse; interstitial and compensatory emphysema',
'Respiratory failure, insufficiency, arrest',
'Respiratory insufficiency',
'Other diseases of lung',
'Other symptoms of respiratory system',
'Shortness of breath',
'Cough',
'Other dyspnea',
'Respiratory abnormalities',
'Abnormal findings examination of lungs',
'Abnormal sputum',
'Hemoptysis',
'Other diseases of respiratory system, not elsewhere classified',
'Other diseases of respiratory system, NEC',
'Disorders of tooth development',
'Disturbances in tooth eruption',
'Diseases of hard tissues of teeth',
'Dental caries',
'Diseases of pulp and periapical tissues',
'Periapical abscess',
'Gingival and periodontal diseases',
'Periodontitis (acute or chronic)',
'Chronic periodontitis',
'Other diseases of the teeth and supporting structures',
'Diseases of the jaws',
'Diseases of the salivary glands',
'Diseases of the oral soft tissues, excluding lesions specific for gingiva and tongue',
'Diseases and other conditions of the tongue',
'Diseases of esophagus',
'Esophagitis, GERD and related diseases',
'GERD',
'Ulcer of esophagus',
'Reflux esophagitis',
'Esophageal bleeding (varices/hemorrhage)',
'Stricture and stenosis of esophagus',
'Heartburn',
'Peptic ulcer (excl. esophageal)',
'Gastric ulcer',
'Duodenal ulcer',
'Dysphagia',
'Gastritis and duodenitis',
'Acute gastritis',
'Duodenitis',
'Other specified gastritis',
'Other disorders of stomach and duodenum',
'Appendiceal conditions',
'Appendicitis',
'Acute appendicitis',
'Abdominal hernia',
'Inguinal hernia',
'Diaphragmatic hernia',
'Umbilical hernia',
'Ventral hernia',
'Inflammatory bowel disease and other gastroenteritis and colitis',
'Regional enteritis',
'Ulcerative colitis',
'Ulceration of the lower GI tract',
'Intestinal malabsorption (non-celiac)',
'Celiac disease',
'Noninfectious gastroenteritis',
'Ileostomy status',
'Intestinal obstruction without mention of hernia',
'Peritoneal or intestinal adhesions',
'Other intestinal obstruction',
'Symptoms involving digestive system',
'Flatulence',
'Diverticulosis and diverticulitis',
'Diverticulosis',
'Constipation',
'Functional digestive disorders',
'Irritable Bowel Syndrome',
'Abnormal findings on exam of gastrointestinal tract/ abdominal area',
'Personal history of diseases of digestive system',
'Anal and rectal conditions',
'Anal and rectal polyp',
'Peritonitis and retroperitoneal infections',
'Other disorders of peritoneum',
'Peritoneal adhesions (postoperative) (postinfection)',
'Other disorders of intestine',
'Chronic liver disease and cirrhosis',
'Other chronic nonalcoholic liver disease',
'Liver abscess and sequelae of chronic liver disease',
'Ascites (non malignant)',
'Other disorders of liver',
'Jaundice (not of newborn)',
'Abnormal results of function study of liver',
'Cholelithiasis and cholecystitis',
'Cholelithiasis',
'Cholelithiasis with acute cholecystitis',
'Cholelithiasis with other cholecystitis',
'Calculus of bile duct',
'Cholecystitis without cholelithiasis',
'Other biliary tract disease',
'Obstruction of bile duct',
'Other disorders of gallbladder',
'Other disorders of biliary tract',
'Diseases of pancreas',
'Acute pancreatitis',
'Gastrointestinal hemorrhage',
'Hematemesis',
'Blood in stool',
'Hemorrhage of rectum and anus',
'Hemorrhage of gastrointestinal tract',
'Other symptoms involving abdomen and pelvis',
'Nonspecific abnormal findings in stool contents',
'Nephritis; nephrosis; renal sclerosis',
'Glomerulonephritis',
'Renal failure',
'Acute renal failure',
'Renal failure NOS',
'Chronic renal failure [CKD]',
'Other disorders of the kidney and ureters',
'Cyst of kidney, acquired',
'Stricture/obstruction of ureter',
'Pyelonephritis',
'Urinary tract infection',
'Cystitis and urethritis',
'Cystitis',
'Chronic cystitis',
'Hematuria',
'Urinary calculus',
'Calculus of kidney',
'Calculus of ureter',
'Renal colic',
'Hydronephrosis',
'Other disorders of bladder',
'Bladder neck obstruction',
'Functional disorders of bladder',
'Other disorders of urethra and urinary tract',
'Urethral stricture (not specified as infectious)',
'Abnormal findings on examination of urine',
'Other symptoms/disorders or the urinary system',
'Urinary obstruction',
'Retention of urine',
'Dysuria',
'Urinary incontinence',
'Frequency of urination and polyuria',
'Other abnormality of urination',
'Hyperplasia of prostate',
'Inflammatory diseases of prostate',
'Prostatitis',
'Chronic prostatitis',
'Orchitis and epididymitis',
'Other disorders of prostate',
'Other disorders of testis',
'Hydrocele',
'Disorders of penis',
'Redundant prepuce and phimosis/BXO',
'Other disorders of male genital organs',
'Benign mammary dysplasias',
'Benign neoplasm of breast',
'Other specified benign mammary dysplasias',
'Abnormal findings on mammogram or breast exam',
'Lump or mass in breast',
'Breast conditions, congenital or relating to hormones',
'Other nonmalignant breast conditions',
'Inflammatory diseases of female pelvic organs',
'Pelvic peritoneal adhesions, female (postoperative) (postinfection)',
'Pelvic inflammatory disease (PID)',
'Inflammatory disease of cervix, vagina, and vulva',
'Cervicitis and endocervicitis',
'Endometriosis',
'Genital prolapse',
'Prolapse of vaginal walls',
'Uterine/Uterovaginal prolapse',
'Noninflammatory female genital disorders',
'Noninflammatory disorders of ovary, fallopian tube, and broad ligament',
'Disorders of uterus, NEC',
'Noninflammatory disorders of cervix',
'Noninflammatory disorders of vagina',
'Noninflammatory disorders of vulva and perineum',
'Endometrial hyperplasia',
'Polyp of female genital organs',
'Polyp of corpus uteri',
'Mucous polyp of cervix',
'Hypertrophy of female genital organs',
'stress incontinence, female',
'Pain and other symptoms associated with female genital organs',
'Dyspareunia',
'Disorders of menstruation and other abnormal bleeding from female genital tract',
'Irregular menstrual cycle/bleeding',
'Excessive or frequent menstruation',
'Irregular menstrual cycle',
'Irregular menstrual bleeding',
'Dysmenorrhea',
'Infertility, female',
'Menopausal and postmenopausal disorders',
'Postmenopausal bleeding',
'Postmenopausal atrophic vaginitis',
'Ovarian cyst',
'Miscarriage; stillbirth',
'Missed abortion/Hydatidiform mole',
'Hemorrhage during pregnancy; childbirth and postpartum',
'Placenta previa and abruptio placenta',
'Early or threatened labor; hemorrhage in early pregnancy',
'Hemorrhage in early pregnancy',
'Hypertension complicating pregnancy, childbirth, and the puerperium',
'Late pregnancy and failed induction',
'Other complications of pregnancy NEC',
'Normal delivery',
'Malposition and malpresentation of fetus or obstruction',
'Problems associated with amniotic cavity and membranes',
'Abnormality of organs and soft tissues of pelvis complicating pregnancy, childbirth, or the puerperium',
'Known or suspected fetal abnormality affecting management of mother',
'Fetal distress and abnormal forces of labor',
'Obstetrical/birth trauma',
'Complications of labor and delivery NEC',
'Superficial cellulitis and abscess',
'Cellulitis and abscess of arm/hand',
'Other local infections of skin and subcutaneous tissue',
'Carbuncle and furuncle',
'Symptoms affecting skin',
'Rash and other nonspecific skin eruption',
'Localized superficial swelling, mass, or lump',
'Disturbance of skin sensation',
'Disorder of skin and subcutaneous tissue NOS',
'Dyschromia and Vitiligo',
'Erythematous conditions',
'Psoriasis and related disorders',
'Psoriasis',
'Other hypertrophic and atrophic conditions of skin',
'Scar conditions and fibrosis of skin',
'Degenerative skin conditions and other dermatoses',
'Actinic keratosis',
'Seborrheic keratosis',
'Diseases of nail, NOS',
'Ingrowing nail',
'Diseases of hair and hair follicles',
'Diseases of sebaceous glands',
'Sebaceous cyst',
'Chronic ulcer of skin',
'Decubitus ulcer',
'Diffuse diseases of connective tissue',
'Rheumatoid arthritis and other inflammatory polyarthropathies',
'Rheumatoid arthritis',
'Other inflammatory spondylopathies',
'Other arthropathies',
'Unspecified monoarthritis',
'Arthropathy NOS',
'Polymyalgia Rheumatica',
'Spinal stenosis',
'Spondylosis and allied disorders',
'Spondylosis without myelopathy',
'Intervertebral disc disorders',
'Degeneration of intervertebral disc',
'Other and unspecified disc disorder',
'Peripheral enthesopathies and allied syndromes',
'Enthesopathy',
'Bursitis',
'Other disorders of synovium, tendon, and bursa',
'Synovitis and tenosynovitis',
'Ganglion and cyst of synovium, tendon, and bursa',
'Disorders of muscle, ligament, and fascia',
'Fasciitis',
"Contracture of palmar fascia [Dupuytren's disease]",
'Other disorders of soft tissues',
'Rheumatism, unspecified and fibrositis',
'Other disorders of bone and cartilage',
'Malunion and nonunion of fracture',
'Acquired foot deformities',
'Acquired toe deformities',
'Hammer toe (acquired)',
'Hallux rigidus',
'Hallux valgus (Bunion)',
'Other acquired deformities of limbs',
'Curvature of spine',
'Kyphoscoliosis and scoliosis',
'Other acquired musculoskeletal deformity',
'Acquired spondylolisthesis',
'Osteoarthrosis',
'Osteoarthritis; localized',
'Osteoarthrosis, localized, primary',
'Osteoarthrosis NOS',
'Symptoms and disorders of the joints',
'Joint effusions',
'Derangement of joint, non-traumatic',
'Other derangement of joint',
'Osteoporosis, osteopenia and pathological fracture',
'Osteoporosis',
'Osteoporosis NOS',
'Pain in joint',
'Cardiac and circulatory congenital anomalies',
'Cardiac congenital anomalies',
'Congenital anomalies of great vessels',
'Genitourinary congenital anomalies',
'Congenital anomalies of urinary system',
'Back pain',
'Cervicalgia',
'Sciatica',
'Neuralgia, neuritis, and radiculitis NOS',
'Musculoskeletal symptoms referable to limbs',
'Swelling of limb',
'Pain in limb',
'Symptoms involving nervous and musculoskeletal systems',
'Edema',
'Fever of unknown origin',
'Abdominal pain',
'Syncope and collapse',
'Nausea and vomiting',
'Other abnormal blood chemistry',
'Malaise and fatigue',
'Fracture of lower limb',
'Fracture of neck of femur',
'Fracture of unspecified part of femur',
'Fracture of tibia and fibula',
...]focal_disease = {
"opentarget_name": "triglyceride",
"opentarget_id": "EFO_0004530",
"df_query_string": "Triglycerides",
}
# focal_disease = {
# "opentarget_name": "",
# "opentarget_id": "",
# "df_query_string": "Body mass index (BMI)",
# }
# focal_disease = {
# "opentarget_name": "arthritis",
# "opentarget_id": "HP_0001370",
# "df_query_string": "Rheumatoid arthritis",
# }
# focal_disease = {
# "opentarget_name": "breast",
# "opentarget_id": "EFO_0003869",
# "df_query_string": "Breast cancer",
# }
# focal_disease = {
# "opentarget_name": "",
# "opentarget_id": "",
# "df_query_string": "Colon cancer",
# }
# trait_df_noRx.query("description == 'Body mass index (BMI)'")
trait_df_noRx.query(f"description == '{focal_disease['df_query_string']}'")
# trait_df_noRx.query("description == 'Systolic blood pressure, combined automated + manual reading, adjusted by medication'")
# trait_df_noRx.query("description == 'Rheumatoid arthritis'")
# trait_df_noRx.query("description == 'Breast cancer'")
# trait_df_noRx.query("description == 'Cancer of prostate'")
| zindex | trait_type | phenocode | pheno_sex | coding | modifier | description | description_more | coding_description | category | BIN_QT | n_cases_EUR | n_controls_EUR | N | Neff | filename | aws_link | estimates.final.h2_observed | long_description | short_description | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1704 | 1705 | biomarkers | 30870 | both_sexes | NaN | irnt | Triglycerides | NaN | NaN | Biological samples > Assay results > Blood ass... | QT | 400639 | NaN | 400639 | 400639.0 | biomarkers-30870-both_sexes-irnt.tsv.bgz | https://pan-ukb-us-east-1.s3.amazonaws.com/sum... | 0.177 | Triglycerides | Triglycerides |
zindex = 1705
trait_indices = np.array(trait_df_noRx.index)
tidx = np.searchsorted(trait_indices, zindex - 1)
top_factor = np.argsort(cos2_pheno[tidx,:])[::-1][0]
# top_factor_score = cos2_pheno[tidx, top_factor]
top_traits_idx = np.argsort(contribution_pheno[:,top_factor])[::-1]
top_traits_name = trait_df_noRx.loc[trait_indices[top_traits_idx]]['short_description'].to_list()
top_traits_score = contribution_pheno[top_traits_idx, top_factor]
top_variant_idx = np.argsort(contribution_variant[:, top_factor])[::-1][:20]
top_variant_df = variant_df.loc[zscore_df.index.to_numpy()[top_variant_idx]]
top_variant_score = contribution_variant[top_variant_idx, top_factor]fig = plt.figure(figsize = (12, 8))
ax1 = fig.add_subplot(111)
xvals = np.arange(cos2_pheno.shape[0])
yvals = cos2_pheno[tidx,:]
ax1.bar(xvals, yvals, align = 'center', width = 0.1)
for side in ['top', 'right']:
ax1.spines[side].set_visible(False)
ax1.tick_params(bottom=False)
ax1.set_ylabel(f"Importance of hidden factors")
ax1.set_xlabel(f"Index")
ax1.set_xlim([-10, 100])
plt.show()
# cos2_pheno = compute_cos(U)
# contribution_pheno = compute_contribution(U)
# cos2_pheno = get_cos2_scores(loadings)
# contribution_pheno = get_contribution_scores(loadings)
fig = plt.figure(figsize = (8, 12))
ax1 = fig.add_subplot(111)
n_plot_traits = 20
xvals = top_traits_score[:n_plot_traits]
yvals = np.arange(n_plot_traits)[::-1]
ax1.barh(yvals, xvals, align = 'center', height = 0.7)
ax1.set_yticks(yvals)
ax1.set_yticklabels(top_traits_name[:n_plot_traits])
for side in ['top', 'right', 'left']:
ax1.spines[side].set_visible(False)
ax1.tick_params(left=False)
ax1.set_xlabel(f"Contribution of traits to PC{top_factor + 1}")
plt.show()
We can look up which factors qualify as top factor for which disease.
top_factor_dict = {i : list() for i in range(cos2_pheno.shape[0])}
for i, trait_name in enumerate(trait_df_noRx['description'].to_list()):
top_factor = np.argsort(cos2_pheno[i, :])[::-1][0]
top_factor_dict[top_factor].append(trait_name)top_factor_dict{0: ['B98 Other specified infectious agents as the cause of diseases classified to other chapters',
'D13 Benign neoplasm of other and ill-defined parts of digestive system',
'E66 Obesity',
'G93 Other disorders of brain',
'J92 Pleural plaque',
'K64 Haemorrhoids and perianal venous thrombosis',
'M18 Arthrosis of first carpometacarpal joint',
'N99 Postprocedural disorders of genito-urinary system, not elsewhere classified',
'O04 Medical abortion',
'O34 Maternal care for known or suspected abnormality of pelvic organs',
'O47 False labour',
'R09 Other symptoms and signs involving the circulatory and respiratory systems',
'R45 Symptoms and signs involving emotional state',
'R87 Abnormal findings in specimens from female genital organs',
'W11 Fall on and from ladder',
'X50 Overexertion and strenuous or repetitive movements',
'X59 Exposure to unspecified factor',
'Y42 Hormones and their synthetic substitutes and antagonists, not elsewhere classified',
'Y45 Analgesics, antipyretics and anti-inflammatory drugs',
'Y84 Other medical procedures as the cause of abnormal reaction of the patient, or of later complication, without mention of misadventure at the time of the procedure',
'Z01 Other special examinations and investigations of persons without complaint or reported diagnosis',
'Z30 Contraceptive management',
'Z36 Antenatal screening',
'Z48 Other surgical follow-up care',
'Z71 Persons encountering health services for other counselling and medical advice, not elsewhere classified',
'Z94 Transplanted organ and tissue status',
'Z97 Presence of other devices',
'Viral warts & HPV',
'Infection/inflammation of internal prosthetic device; implant; and graft',
'Foreign body injury',
'Crushing or internal injury to organs',
'Cancer of prostate',
'Myeloproliferative disease',
'Other benign neoplasm of connective and other soft tissue',
'Anorexia',
'Overweight, obesity and other hyperalimentation',
'Obesity',
'Other diseases of blood and blood-forming organs',
'Other specified nonpsychotic and/or transient mental disorders',
'Schizophrenia and other psychotic disorders',
'Other cerebral degenerations',
"Parkinson's disease",
'Extrapyramidal disease and abnormal movement disorders',
'Ill-defined descriptions and complications of heart disease',
'Polyarteritis nodosa and allied conditions',
'Other dyspnea',
'Diseases of the jaws',
'Heartburn',
'Acute gastritis',
'Ulceration of the lower GI tract',
'Flatulence',
'Other symptoms involving abdomen and pelvis',
'Nonspecific abnormal findings in stool contents',
'Breast conditions, congenital or relating to hormones',
'Pelvic inflammatory disease (PID)',
'Infertility, female',
'Postmenopausal atrophic vaginitis',
'Hemorrhage in early pregnancy',
'Malposition and malpresentation of fetus or obstruction',
'Abnormality of organs and soft tissues of pelvis complicating pregnancy, childbirth, or the puerperium',
'Dyschromia and Vitiligo',
'Fracture of clavicle or scapula',
'Fracture of vertebral column without mention of spinal cord injury',
'Skull and face fracture and other intercranial injury',
'Injuries to the nervous system',
'Poisoning/allergy of sulfonamides',
'Cancer code, self-reported',
'Cancer code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Illnesses of father',
'Illnesses of father',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'Albumin',
'Apolipoprotein A',
'HDL cholesterol',
'Lipoprotein A',
'Oestradiol',
'Phosphate',
'Rheumatoid factor',
'SHBG',
'Testosterone',
'Urate',
'Vitamin D',
'Portion size',
'Duration of strenuous sports',
'Low calorie drink intake',
'Fizzy drink intake',
'Squash intake',
'Dairy smoothie intake',
'Intake of sugar added to coffee',
'Standard tea intake',
'Rooibos tea intake',
'Green tea intake',
'Other tea intake',
'Intake of sugar added to tea',
'Milk intake',
'Flavoured milk intake',
'Hot chocolate intake',
'Fortified wine intake',
'Spirits intake',
'Porridge intake',
'Sweetened cereal intake',
'Plain cereal intake',
'Whole-wheat cereal intake',
'Other cereal intake',
'Intake of sugar added to cereal',
'Intake of artificial sweetener added to cereal',
'Bap intake',
'Garlic bread intake',
'Number of other bread types with butter/margarine',
'Double crust pastry intake',
'Single crust pastry intake',
'Pizza intake',
'Yorkshire pudding intake',
'Danish pastry intake',
'Scone intake',
'Milk-based pudding intake',
'Cheesecake intake',
'Chocolate bar intake',
'Milk chocolate intake',
'Chocolate sweet intake',
'Sweets intake',
'Chocolate-covered biscuits intake',
'Chocolate biscuits intake',
'Sweet biscuits intake',
'Cereal bar intake',
'Other sweets intake',
'Salted peanuts intake',
'Salted nuts intake',
'Unsalted nuts intake',
'Seeds intake',
'Crisp intake',
'Other savoury snack intake',
'Canned soup intake',
'Wholemeal pasta intake',
'Brown rice intake',
'Couscous intake',
'Low fat hard cheese intake',
'Low fat cheese spread intake',
'Other cheese intake',
'Whole egg intake',
'Omelette intake',
'Eggs in sandwiches intake',
'Pork intake',
'Lamb intake',
'Crumbed or deep-fried poultry intake',
'Breaded fish intake',
'Battered fish intake',
'White fish intake',
'Baked bean intake',
'Mashed potato intake',
'Mixed vegetable intake',
'Broad bean intake',
'Broccoli intake',
'Leek intake',
'Parsnip intake',
'Pea intake',
'Sprouts intake',
'Sweetcorn intake',
'Sweet potato intake',
'Tinned tomato intake',
'Turnip/swede intake',
'Watercress intake',
'Mixed fruit intake',
'Satsuma intake',
'Peach/nectarine intake',
'Pineapple intake',
'Plum intake',
'Time spent doing moderate physical activity',
'Time spent doing light physical activity',
'Difference in mobile phone use compared to two years previously',
'Past tobacco smoking',
'Cooked vegetable intake',
'Number of operations, self-reported',
'Tea intake',
'Comparative body size at age 10',
'Facial ageing',
'Hour-of-day questionnaire completed',
'Duration of questionnaire',
'Cascot confidence score',
'Frequency of failure to fulfil normal expectations due to drinking alcohol in last year',
'Frequency of memory loss due to drinking alcohol in last year',
'Age when known person last commented about drinking habits',
'Ever been injured or injured someone else through drinking alcohol',
'Maximum frequency of taking cannabis',
'Age when last took cannabis',
'Age when first had unusual or psychotic experience',
'Distress caused by unusual or psychotic experiences',
'Frequency of unusual or psychotic experiences in past year',
'Number of times self-harmed',
'Felt loved as a child',
'Longest period of mania or irritability',
'Body mass index (BMI)',
'Weight',
'Age at recruitment',
'Age hayfever or allergic rhinitis diagnosed by doctor',
'Age asthma diagnosed by doctor',
'Plays computer games',
'Years of cough on most days',
'Years of bringing up phlegm/sputum/mucus on most days',
'Period spent working mix of day and night shifts',
'Usual length of each night shift during mixed shift periods',
'Rest days during mixed shift periods',
'Number of gap periods',
'Year gap ended',
'Use of sun/uv protection',
'Weight',
'Body fat percentage',
'Whole body fat mass',
'Whole body fat-free mass',
'Whole body water mass',
'Body mass index (BMI)',
'Basal metabolic rate',
'Impedance of whole body',
'Impedance of leg (right)',
'Impedance of leg (left)',
'Impedance of arm (right)',
'Impedance of arm (left)',
'Leg fat mass (right)',
'Leg fat-free mass (right)',
'Leg predicted mass (right)',
'Leg fat mass (left)',
'Leg fat-free mass (left)',
'Leg predicted mass (left)',
'Arm fat percentage (right)',
'Arm fat mass (right)',
'Arm fat-free mass (right)',
'Arm predicted mass (right)',
'Arm fat percentage (left)',
'Arm fat mass (left)',
'Arm fat-free mass (left)',
'Arm predicted mass (left)',
'Trunk fat percentage',
'Trunk fat mass',
'Trunk fat-free mass',
'Trunk predicted mass',
'Relative age of first facial hair',
'Relative age voice broke',
'Years since last breast cancer screening / mammogram',
'Age when periods started (menarche)',
'Number of unsuccessful stop-smoking attempts',
'Likelihood of resuming smoking',
'Basophill percentage',
'Creatinine (enzymatic) in urine',
'Ankle spacing width',
'Weight, manual entry',
'Job involves night shift work',
'Wants to stop smoking',
'Smoking compared to 10 years previous',
'Age last used hormone-replacement therapy (HRT)',
'Age angina diagnosed',
'Duration of other exercises',
'Lifetime number of same-sex sexual partners',
'Age when last ate meat',
'Length of menstrual cycle',
'Time since last prostate specific antigen (PSA) test',
'Number of stillbirths',
'Number of spontaneous miscarriages',
'Number of incorrect matches in round',
'Age emphysema/chronic bronchitis diagnosed',
'Time to complete round',
'Age at death',
'Age deep-vein thrombosis (DVT, blood clot in leg) diagnosed',
'Ankle spacing width (left)',
'Ankle spacing width (right)',
'Time to answer',
'Average monthly beer plus cider intake',
'Average monthly fortified wine intake',
'Average monthly intake of other alcoholic drinks',
'Work/job satisfaction',
'Age cataract diagnosed',
'Waist circumference',
'Tinnitus',
'Tinnitus severity/nuisance',
'Loud music exposure frequency',
'Hip circumference',
'Number of older siblings',
'6mm asymmetry angle (right)',
'logMAR, final (right)',
'logMAR, final (left)',
'Index of best refractometry result (right)',
'3mm index of best keratometry results (right)',
'6mm index of best keratometry results (right)',
'Index of best refractometry result (left)',
'3mm index of best keratometry results (left)',
'6mm index of best keratometry results (left)',
'Number of unenthusiastic/disinterested episodes',
'Maximum heart rate during fitness test',
'Time employed in main current job',
'Number of days/week walked 10+ minutes',
'Number of days/week of moderate physical activity 10+ minutes',
'Number of days/week of vigorous physical activity 10+ minutes',
'Frequency of strenuous sports in last 4 weeks',
'Estimated glomerular filtration rate, serum creatinine + cystain C'],
1: ['E78 Disorders of lipoprotein metabolism and other lipidaemias',
'F17 Mental and behavioural disorders due to use of tobacco',
'G56 Mononeuropathies of upper limb',
'I20 Angina pectoris',
'I21 Acute myocardial infarction',
'I25 Chronic ischaemic heart disease',
'M13 Other arthritis',
'M15 Polyarthrosis',
'O03 Spontaneous abortion',
'R07 Pain in throat and chest',
'V18 Pedal cyclist injured in noncollision transport accident',
'W00 Fall on same level involving ice and snow',
'Z12 Special screening examination for neoplasms',
'Z35 Supervision of high-risk pregnancy',
'Z82 Family history of certain disabilities and chronic diseases leading to disablement',
'Benign neoplasm of lip, oral cavity, and pharynx',
'Benign neoplasm of ovary',
'Disorders of lipoid metabolism',
'Hyperlipidemia',
'Hypercholesterolemia',
'Tobacco use disorder',
'Other headache syndromes',
'Other peripheral nerve disorders',
'Hypertension',
'Essential hypertension',
'Ischemic Heart Disease',
'Unstable angina (intermediate coronary syndrome)',
'Myocardial infarction',
'Angina pectoris',
'Coronary atherosclerosis',
'Other chronic ischemic heart disease, unspecified',
'Nonspecific chest pain',
'Precordial pain',
'Dysphagia',
'Late pregnancy and failed induction',
'Osteoarthrosis NOS',
'Cancer code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Illnesses of father',
'Illnesses of father',
'Illnesses of father',
'Illnesses of father',
'Illnesses of father',
'Illnesses of father',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'Alkaline phosphatase',
'Alanine aminotransferase',
'Aspartate aminotransferase',
'C-reactive protein',
'Gamma glutamyltransferase',
'Glucose',
'Glycated haemoglobin (HbA1c)',
'Total bilirubin',
'Alcohol',
'Drinking water intake',
'Orange juice intake',
'Grapefruit juice intake',
'Pure fruit/vegetable juice intake',
'Fruit smoothie intake',
'Filtered coffee intake',
'Cappuccino intake',
'Latte intake',
'Espresso intake',
'Herbal tea intake',
'Red wine intake',
'Rose wine intake',
'White wine intake',
'Muesli intake',
'Oat crunch intake',
'Bran cereal intake',
'Frequency of light DIY in last 4 weeks',
'Naan bread intake',
'Oatcakes intake',
'Crumble intake',
'Pulse rate, automated reading',
'Croissant intake',
'Yogurt intake',
'Ice-cream intake',
'Other milk-based pudding intake',
'Fruitcake intake',
'Cake intake',
'Sponge pudding intake',
'Other dessert intake',
'Dark chocolate intake',
'Olives intake',
'Powdered/instant soup intake',
'Homemade soup intake',
'White pasta intake',
'White rice intake',
'Hard cheese intake',
'Soft cheese intake',
'Blue cheese intake',
'Mozzarella intake',
'Sausage intake',
'Liver intake',
'Frequency of friend/family visits',
'Tinned tuna intake',
'Oily fish intake',
'Pulses intake',
'Vegetable pieces intake',
'Coleslaw intake',
'Side salad intake',
'Avocado intake',
'Green bean intake',
'Butternut squash intake',
'Cabbage/kale intake',
'Celery intake',
'Courgette intake',
'Garlic intake',
'Lettuce intake',
'Mushroom intake',
'Onion intake',
'Spinach intake',
'Other vegetables intake',
'Stewed fruit intake',
'Prune intake',
'Dried fruit intake',
'Apple intake',
'Berry intake',
'Cherry intake',
'Grapefruit intake',
'Mango intake',
'Melon intake',
'Orange intake',
'Pear intake',
'Other fruit intake',
'Time spend outdoors in summer',
'Time spent watching television (TV)',
'Time spent using computer',
'Drive faster than motorway speed limit',
'Morning/evening person (chronotype)',
'Nap during day',
'Sleeplessness / insomnia',
'QRS duration',
'Current tobacco smoking',
'Smoking/smokers in household',
'Exposure to tobacco smoke at home',
'Exposure to tobacco smoke outside home',
'Place of birth in UK - north co-ordinate',
'Salad / raw vegetable intake',
'Place of birth in UK - east co-ordinate',
'Fresh fruit intake',
'Dried fruit intake',
'Number of self-reported non-cancer illnesses',
'Poultry intake',
'Number of treatments/medications taken',
'Lamb/mutton intake',
'Cheese intake',
'Bread intake',
'Cereal intake',
'Hot drink temperature',
'Water intake',
'Variation in diet',
'Alcohol intake frequency.',
'Average weekly red wine intake',
'Average weekly champagne plus white wine intake',
'Average weekly fortified wine intake',
'Alcohol intake versus 10 years previously',
'Comparative height size at age 10',
'Childhood sunburn occasions',
"Father's age at death",
"Mother's age",
'Number of full brothers',
'Number of full sisters',
'Townsend deprivation index at recruitment',
'Sitting height',
'Fluid intelligence score',
'Prospective memory result',
'Birth weight',
'Home location at assessment - east co-ordinate (rounded)',
'Number of diet questionnaires completed',
'Number of fluid intelligence questions attempted within time limit',
'Forced expiratory volume in 1-second (FEV1), Best measure',
'Forced vital capacity (FVC), Best measure',
'Forced expiratory volume in 1-second (FEV1), predicted',
'Forced expiratory volume in 1-second (FEV1), predicted percentage',
'Frequency of drinking alcohol',
'Ever taken cannabis',
'Someone to take to doctor when needed as a child',
'Been in a confiding relationship as an adult',
'Able to pay rent/mortgage as an adult',
'Able to confide',
'Age first had sexual intercourse',
'Overall health rating',
'Year of birth',
'Year ended full time education',
'Year job started',
'Year job ended',
'Home location - east co-ordinate (rounded)',
'Leg fat percentage (right)',
'Leg fat percentage (left)',
'Most recent bowel cancer screening',
'Birth weight of first child',
'Age at first live birth',
'Age at last live birth',
'Age started oral contraceptive pill',
'Age when last used oral contraceptive pill',
'Age at hysterectomy',
'Age started smoking in former smokers',
'Age stopped smoking',
"Father's age",
'White blood cell (leukocyte) count',
'Potassium in urine',
'Sodium in urine',
'Forced vital capacity (FVC)',
'Forced expiratory volume in 1-second (FEV1)',
'Peak expiratory flow (PEF)',
'Seating box height',
'Year of birth',
'Age started smoking in current smokers',
'Time from waking to first cigarette',
'Ever tried to stop smoking',
"Mother's age at death",
'Age started hormone-replacement therapy (HRT)',
'Age at menopause (last menstrual period)',
'Year immigrated to UK (United Kingdom)',
'Number of pregnancy terminations',
'Age of primiparous women at birth of child',
'Age at bilateral oophorectomy (both ovaries removed)',
'Age heart attack diagnosed',
'Number of correct matches in round',
'Number of times snap-button pressed',
'Age stroke diagnosed',
'Pulse wave peak to peak time',
'Maximum digits remembered correctly',
'Average monthly red wine intake',
'Average monthly champagne plus white wine intake',
'Health satisfaction',
'Financial situation satisfaction',
'Hand grip strength (left)',
'Number of depression episodes',
'Private healthcare',
'Hand grip strength (right)',
'Noisy workplace',
'Standing height',
'Seated height',
'3mm asymmetry index (left)',
'6mm asymmetry index (right)',
'3mm asymmetry index (right)',
'Longest period of unenthusiasm / disinterest',
'Leg pain on walking : action taken',
'ECG, load',
'ECG, number of stages in a phase',
'Maximum workload during fitness test',
'Number of trend entries',
'Duration of fitness test',
'Number in household',
'Number of vehicles in household',
'Average total household income before tax',
'Frequency of travelling from home to job workplace',
'Job involves mainly walking or standing',
'Job involves heavy manual or physical work',
'Job involves shift work',
'Age completed full time education',
'Non-cancer illness year/age first occurred',
'Usual walking pace',
'Frequency of stair climbing in last 4 weeks',
'Duration walking for pleasure',
'Indirect bilirubin',
'pheno 48 / pheno 49'],
2: ['G57 Mononeuropathies of lower limb',
'K60 Fissure and fistula of anal and rectal regions',
'K61 Abscess of anal and rectal regions',
'M22 Disorders of patella',
'M75 Shoulder lesions',
'M79 Other soft tissue disorders, not elsewhere classified',
'R10 Abdominal and pelvic pain',
'Complications of surgical and medical procedures',
'Hypertension complicating pregnancy, childbirth, and the puerperium',
'Other inflammatory spondylopathies',
'Pain in limb',
'Abdominal pain',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Illnesses of father',
'Illnesses of father',
'Illnesses of father',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'Illnesses of mother',
'IGF-1',
'Weekly usage of mobile phone in last 3 months',
'Sleep duration',
'P duration',
'Oily fish intake',
'Salt added to food',
'Average weekly spirits intake',
'Frequency of depressed mood in last 2 weeks',
'Frequency of unenthusiasm / disinterest in last 2 weeks',
'Frequency of tiredness / lethargy in last 2 weeks',
'Falls in the last year',
'Weight change compared with 1 year ago',
'Age high blood pressure diagnosed',
'Diastolic blood pressure, automated reading',
'Systolic blood pressure, automated reading',
'Diastolic blood pressure, automated reading, adjusted by medication',
'Diastolic blood pressure, combined automated + manual reading',
'Diastolic blood pressure, combined automated + manual reading, adjusted by medication',
'Mean arterial pressure, automated reading',
'Mean arterial pressure, automated reading, adjusted by medication',
'Mean arterial pressure, combined automated + manual reading',
'Mean arterial pressure, combined automated + manual reading, adjusted by medication',
'Multi-site chronic pain',
'Pulse pressure, automated reading',
'Pulse pressure, automated reading, adjusted by medication',
'Pulse pressure, combined automated + manual reading',
'Pulse pressure, combined automated + manual reading, adjusted by medication',
'Systolic blood pressure, automated reading, adjusted by medication',
'Systolic blood pressure, combined automated + manual reading',
'Systolic blood pressure, combined automated + manual reading, adjusted by medication',
'Smoking status, ever vs never'],
3: ['I48 Atrial fibrillation and flutter',
'M81 Osteoporosis without pathological fracture',
'W01 Fall on same level from slipping, tripping and stumbling',
'W10 Fall on and from stairs and steps',
'W18 Other fall on same level',
'W19 Unspecified fall',
'Dizziness and giddiness (Light-headedness and vertigo)',
'Atrial fibrillation and flutter',
'Osteoporosis, osteopenia and pathological fracture',
'Osteoporosis',
'Osteoporosis NOS',
'Symptoms involving nervous and musculoskeletal systems',
'Fracture of lower limb',
'Fracture of unspecified part of femur',
'Fracture of upper limb',
'Fracture of humerus',
'Fracture of radius and ulna',
'Fracture of hand or wrist',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Ham intake',
'Banana intake',
'Grape intake',
'Length of mobile phone use',
'Hands-free device/speakerphone use with mobile phone in last 3 month',
'Non-oily fish intake',
'Neuroticism score',
'Microalbumin in urine',
'Heel Broadband ultrasound attenuation, direct entry',
'Heel quantitative ultrasound index (QUI), direct entry',
'Heel bone mineral density (BMD)',
'Heel broadband ultrasound attenuation (left)',
'Heel quantitative ultrasound index (QUI), direct entry (left)',
'Heel bone mineral density (BMD) (left)',
'Heel bone mineral density (BMD) T-score, automated (left)',
'Heel broadband ultrasound attenuation (right)',
'Heel quantitative ultrasound index (QUI), direct entry (right)',
'Heel bone mineral density (BMD) (right)',
'Heel bone mineral density (BMD) T-score, automated (right)',
'Heel bone mineral density (BMD) T-score, automated',
'Distance between home and job workplace'],
4: ['B96 Other bacterial agents as the cause of diseases classified to other chapters',
'D64 Other anaemias',
'E87 Other disorders of fluid, electrolyte and acid-base balance',
'F32 Depressive episode',
'I50 Heart failure',
'I51 Complications and ill-defined descriptions of heart disease',
'J18 Pneumonia, organism unspecified',
'J44 Other chronic obstructive pulmonary disease',
'K59 Other functional intestinal disorders',
'M19 Other arthrosis',
'M47 Spondylosis',
'M54 Dorsalgia',
'N17 Acute renal failure',
'T81 Complications of procedures, not elsewhere classified',
'Y83 Surgical operation and other surgical procedures as the cause of abnormal reaction of the patient, or of later complication, without mention of misadventure at the time of the procedure',
'Z03 Medical observation and evaluation for suspected diseases and conditions',
'Z13 Special screening examination for other diseases and disorders',
'Z22 Carrier of infectious disease',
'Z53 Persons encountering health services for specifie procedures, not carried out',
'Z60 Problems related to social environment',
'Z72 Problems related to lifestyle',
'Z86 Personal history of certain other diseases',
'Z87 Personal history of other diseases and conditions',
'Z88 Personal history of allergy to drugs, medicaments and biologocal substances',
'Z91 Personal history of risk-factors, not elsewhere classified',
'Z92 Personal history of medical treatment',
'Z99 Dependence on enabling machines and devices, not elsewhere classified',
'Bacterial infection NOS',
'Staphylococcus infections',
'Other ill-defined and unknown causes of morbidity and mortality',
'Chemotherapy',
'Disorders of fluid, electrolyte, and acid-base balance',
'Electrolyte imbalance',
'Other anemias',
'Other mental disorder',
'Other forms of chronic heart disease',
'Cardiomegaly',
'Cardiac pacemaker/device in situ',
'Cardiac pacemaker in situ',
'Cardiac dysrhythmias',
'Other specified cardiac dysrhythmias',
'Congestive heart failure; nonhypertensive',
'Congestive heart failure (CHF) NOS',
'Heart failure NOS',
'Other disorders of circulatory system',
'Circulatory disease NEC',
'Pneumonia',
'Bacterial pneumonia',
'Chronic airway obstruction',
'Chronic bronchitis',
'Obstructive chronic bronchitis',
'Bronchiectasis',
'Pleurisy; pleural effusion',
'Respiratory failure, insufficiency, arrest',
'Other symptoms of respiratory system',
'Cough',
'Constipation',
'Functional digestive disorders',
'Renal failure',
'Acute renal failure',
'Erythematous conditions',
'Spondylosis and allied disorders',
'Spondylosis without myelopathy',
'Pain in joint',
'Back pain',
'Cervicalgia',
'Syncope and collapse',
'Nausea and vomiting',
'Malaise and fatigue',
'Hemorrhage or hematoma complicating a procedure',
'Complications of transplants and reattached limbs',
'Complication due to other implant and internal device',
'Open wounds of head; neck; and trunk',
'Poisoning by analgesics, antipyretics, and antirheumatics',
'Opiates and related narcotics causing adverse effects in therapeutic use',
'Poisoning by agents primarily affecting the cardiovascular system',
'Beef intake',
'Bacon intake',
'Prawns intake',
'Ventricular rate',
'Processed meat intake',
'Beef intake',
'Pork intake',
'Ease of skin tanning',
'Year gap started',
'Spells in hospital',
'ECG, heart rate',
'Length of time at current address',
'Pulse rate (during blood-pressure measurement)'],
5: ['Z02 Examination and encounter for administrative purposes',
'Fracture of ankle and foot',
'Duration of light DIY',
'Coffee intake',
'Work hours per week - exact value',
'Frequency of heavy DIY in last 4 weeks',
'Duration of heavy DIY',
'Frequency of other exercises in last 4 weeks',
'Length of working week for main job'],
6: ['Z04 Examination and observation for other reasons',
'Diffuse diseases of connective tissue',
'Swelling of limb',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Triglycerides',
'Reticulocyte percentage',
'Reticulocyte count',
'Mean sphered cell volume',
'High light scatter reticulocyte percentage',
'High light scatter reticulocyte count',
'Albumin/Globulin ratio',
'FEV1/FVC ratio'],
7: ['Z95 Presence of cardiac and vascular implants and grafts',
'Treatment/medication code',
'Treatment/medication code'],
8: ['O32 Maternal care for known or suspected malpresentation of foetus',
'O72 Postpartum haemorrhage',
'Z34 Supervision of normal pregnancy'],
9: ['N18 Chronic renal failure',
'Renal failure NOS',
'Chronic renal failure [CKD]',
'Non-cancer illness code, self-reported',
'Urea',
'Creatinine',
'Cystatin C',
'Estimated glomerular filtration rate, serum creatinine',
'Estimated glomerular filtration rate, cystain C'],
10: ['I27 Other pulmonary heart diseases',
'Paroxysmal ventricular tachycardia',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Physically abused by family as a child',
'Frequency of solarium/sunlamp use',
'3mm weak meridian (left)',
'6mm weak meridian (left)',
'6mm weak meridian (right)',
'3mm weak meridian (right)',
'3mm strong meridian (right)',
'6mm strong meridian (right)',
'6mm strong meridian (left)',
'3mm strong meridian (left)',
'6mm regularity index (right)'],
11: ['Non-cancer illness code, self-reported',
'Longest period spent worried or anxious',
'Age at last episode of depression',
'Frequency of tenseness / restlessness in last 2 weeks',
'Spherical power (right)',
'Spherical power (left)'],
12: ['Amount of alcohol drunk on a typical drinking day',
'Ever had known person concerned about, or recommend reduction of, alcohol consumption',
'Frequency of consuming six or more units of alcohol',
'Red blood cell (erythrocyte) count',
'Mean corpuscular volume',
'Mean corpuscular haemoglobin',
'Mean corpuscular haemoglobin concentration',
'Red blood cell (erythrocyte) distribution width',
'Mean reticulocyte volume',
'Immature reticulocyte fraction'],
13: ['A41 Other septicaemia',
'C78 Secondary malignant neoplasm of respiratory and digestive organs',
'K12 Stomatitis and related lesions',
'K91 Postprocedural disorders of digestive system, not elsewhere classified',
'Y43 Primarily systemic agents',
'Z43 Attention to artificial openings',
'Z45 Adjustment and management of implanted device',
'Z51 Other medical care',
'Z80 Family history of malignant neoplasm',
'Z93 Artificial opening status',
'Z98 Other postsurgical states',
'Septicemia',
'Gram negative septicemia',
'E. coli',
'Postoperative infection',
'Other tests',
'Secondary malignancy of respiratory organs',
'Secondary malignant neoplasm of digestive systems',
'Secondary malignancy of bone',
'Neoplasm of uncertain behavior',
'Leukemia',
'Hyperpotassemia',
'Hypovolemia',
'Other disorders of metabolism',
'Diseases of white blood cells',
'Decreased white blood cell count',
'Noninfectious disorders of lymphatic channels',
'Ileostomy status',
'Ascites (non malignant)',
'Rash and other nonspecific skin eruption',
'Poisoning by primarily systemic agents',
'Sexually molested as a child',
'Belittlement by partner or ex-partner as an adult',
'Physical violence by partner or ex-partner as an adult',
'Sexual interference by partner or ex-partner without consent as an adult',
'Age of stopping smoking'],
14: ['Apolipoprotein B',
'Calcium',
'Cholesterol',
'LDL direct',
'Total protein',
'Fat',
'Saturated fat',
'Retinol',
'Starch',
'Time spent driving',
'Daytime dozing / sleeping (narcolepsy)',
'Skin colour',
'Age started wearing glasses or contact lenses',
'Consecutive night shifts during mixed shift periods',
'Number of children fathered',
'Happiness',
'Family relationship satisfaction',
'LDL direct, adjusted by medication'],
15: ['Treatment/medication code',
'Carrot intake',
'Lifetime number of sexual partners',
'Nitrogen dioxide air pollution; 2010',
'Nitrogen oxides air pollution; 2010',
'Particulate matter air pollution (pm10); 2010',
'Particulate matter air pollution (pm2.5); 2010',
'Particulate matter air pollution (pm2.5) absorbance; 2010',
'Nitrogen dioxide air pollution; 2005',
'Nitrogen dioxide air pollution; 2006',
'Nitrogen dioxide air pollution; 2007',
'Particulate matter air pollution (pm10); 2007',
'Monocyte count',
'Basophill count',
'Pulse rate'],
16: ['Food weight',
'Energy',
'Protein',
'Carbohydrate',
'Polyunsaturated fat',
'Total sugars',
'Englyst dietary fibre',
'Iron',
'Vitamin B6',
'Folate',
'Vitamin C',
'Potassium',
'Magnesium',
'Carotene',
'Calcium',
'Vitamin E',
'Other drink intake',
'Boiled/baked potatoes intake',
'Beetroot intake',
'Cauliflower intake',
'Cucumber intake',
'Fresh tomato intake',
'Eosinophill count',
'Non-albumin protein'],
17: ['C77 Secondary and unspecified malignant neoplasm of lymph nodes',
'C79 Secondary malignant neoplasm of other sites',
'C80 Malignant neoplasm without specification of site',
'D12 Benign neoplasm of colon, rectum, anus and anal canal',
'J45 Asthma',
'M25 Other joint disorders, not elsewhere classified',
'M77 Other enthesopathies',
'Z08 Follow-up examination after treatment for malignant neoplasm',
'Z09 Follow-up examination after treatment for conditions other than malignant neoplasms',
'Z47 Other orthopaedic follow-up care',
'Z85 Personal history of malignant neoplasm',
'Z90 Acquired absence of organs, not elsewhere classified',
'Malignant neoplasm of other and ill-defined sites within the digestive organs and peritoneum',
'Cancer, suspected or other',
'Malignant neoplasm, other',
'Secondary malignant neoplasm',
'Secondary malignancy of lymph nodes',
'Secondary malignant neoplasm of liver',
'Secondary malignancy of brain/spine',
'Asthma',
'Effects radiation NOS',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Direct bilirubin',
'Number of self-reported cancers',
'Reported occurrences of cancer',
'Average monthly spirits intake'],
18: ['Z75 Problems related to medical facilities and other health care',
'Abnormal findings examination of lungs',
'Non-cancer illness code, self-reported',
'Recent restlessness'],
19: ['Particulate matter air pollution 2.5-10um; 2010',
'Traffic intensity on the nearest road',
'Inverse distance to the nearest road',
'Inverse distance to the nearest major road',
'Total traffic load on major roads',
'Sum of road length of major roads within 100m',
'Average daytime sound level of noise pollution',
'Average evening sound level of noise pollution',
'Average night-time sound level of noise pollution',
'Average 16-hour sound level of noise pollution',
'Average 24-hour sound level of noise pollution'],
20: ['Time spent doing vigorous physical activity',
'Time spent outdoors in winter',
'Getting up in morning',
'Average weekly beer plus cider intake',
'Frequency of feeling guilt or remorse after drinking alcohol in last year',
'Impact on normal roles during worst period of anxiety',
'Age at first episode of depression',
'Fraction of day affected during worst episode of depression',
'Duration of worst depression',
'Frequency of depressed days during worst episode of depression',
'Impact on normal roles during worst period of depression',
'Lifetime number of depressed periods',
'General happiness',
'General happiness with own health',
'Belief that own life is meaningful',
'Ever thought that life not worth living',
'Ever contemplated self-harm',
'Felt hated by family member as a child',
'Felt irritable or had angry outbursts in past month',
'Avoided activities or situations because of previous stressful experience in past month',
'Felt distant from other people in past month',
'Repeated disturbing thoughts of stressful experience in past month',
'Felt very upset when reminded of stressful experience in past month',
'Recent easy annoyance or irritability',
'Recent feelings or nervousness or anxiety',
'Recent feelings of inadequacy',
'Recent trouble concentrating on things',
'Recent inability to stop or control worrying',
'Recent feelings of depression',
'Recent poor appetite or overeating',
'Recent feelings of foreboding',
'Recent thoughts of suicide or self-harm',
'Recent lack of interest or pleasure in doing things',
'Recent trouble relaxing',
'Trouble falling or staying asleep, or sleeping too much',
'Recent changes in speed/amount of moving or speaking',
'Recent feelings of tiredness or low energy',
'Recent worrying too much about different things',
'Frequency of difficulty controlling worry during worst period of anxiety',
'Neutrophill count',
'Eosinophill percentage',
'Friendships satisfaction',
'Longest period of depression',
'Duration of walks',
'Duration of moderate activity',
'Duration of vigorous activity',
'Frequency of walking for pleasure in last 4 weeks'],
21: ['E10 Insulin-dependent diabetes mellitus',
'E11 Non-insulin-dependent diabetes mellitus',
'E14 Unspecified diabetes mellitus',
'H36 Retinal disorders in diseases classified elsewhere',
'Diabetes mellitus',
'Type 1 diabetes',
'Type 2 diabetes',
'Type 2 diabetes with ophthalmic manifestations',
'Diabetic retinopathy',
'Hereditary retinal dystrophies',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code',
'Illnesses of father',
'Platelet count',
'Platelet crit',
'Platelet distribution width'],
22: ['R29 Other symptoms and signs involving the nervous and musculoskeletal systems',
'T84 Complications of internal orthopaedic prosthetic devices, implants and grafts',
'Z50 Care involving use of rehabilitation procedures',
'Z96 Presence of other functional implants',
'Other arthropathies',
'Arthropathy NOS',
'Other acquired deformities of limbs',
'Osteoarthrosis',
'Osteoarthritis; localized',
'Osteoarthrosis, localized, primary',
'Neuralgia, neuritis, and radiculitis NOS',
'Complication of internal orthopedic device'],
23: ['C50 Malignant neoplasm of breast',
'D05 Carcinoma in situ of breast',
'K21 Gastro-oesophageal reflux disease',
'K22 Other diseases of oesophagus',
'K29 Gastritis and duodenitis',
'K31 Other diseases of stomach and duodenum',
'K44 Diaphragmatic hernia',
'K74 Fibrosis and cirrhosis of liver',
'M17 Gonarthrosis [arthrosis of knee]',
'M23 Internal derangement of knee',
'Z42 Follow-up care involving plastic surgery',
'Breast cancer',
'Breast cancer [female]',
'Malignant neoplasm of female breast',
'Acquired absence of breast',
'Benign neoplasm of other parts of digestive system',
'Hypopotassemia',
'Diseases of esophagus',
'Esophagitis, GERD and related diseases',
'GERD',
'Ulcer of esophagus',
'Reflux esophagitis',
'Esophageal bleeding (varices/hemorrhage)',
'Stricture and stenosis of esophagus',
'Gastritis and duodenitis',
'Duodenitis',
'Other specified gastritis',
'Other disorders of stomach and duodenum',
'Abdominal hernia',
'Diaphragmatic hernia',
'Personal history of diseases of digestive system',
'Liver abscess and sequelae of chronic liver disease',
'Hematemesis',
'Blood in stool',
'Unspecified monoarthritis',
'Enthesopathy',
'Internal derangement of knee'],
24: ['Home location at assessment - north co-ordinate (rounded)',
'Home location - north co-ordinate (rounded)',
'Haemoglobin concentration',
'Haematocrit percentage'],
25: ['Treatment/medication code',
'Lymphocyte count',
'Lymphocyte percentage',
'Neutrophill percentage'],
26: ['D25 Leiomyoma of uterus',
'N85 Other noninflammatory disorders of uterus, except cervix',
'N88 Other noninflammatory disorders of cervix uteri',
'N92 Excessive, frequent and irregular menstruation',
'N93 Other abnormal uterine and vaginal bleeding',
'Benign neoplasm of uterus',
'Uterine leiomyoma',
'Disorders of uterus, NEC',
'Noninflammatory disorders of cervix',
'Disorders of menstruation and other abnormal bleeding from female genital tract',
'Irregular menstrual cycle/bleeding',
'Excessive or frequent menstruation',
'Irregular menstrual cycle',
'Irregular menstrual bleeding',
'Dysmenorrhea',
'Minimum carotid IMT (intima-medial thickness) at 120 degrees',
'Mean carotid IMT (intima-medial thickness) at 120 degrees',
'Maximum carotid IMT (intima-medial thickness) at 120 degrees',
'Minimum carotid IMT (intima-medial thickness) at 150 degrees',
'Mean carotid IMT (intima-medial thickness) at 150 degrees',
'Maximum carotid IMT (intima-medial thickness) at 150 degrees',
'Minimum carotid IMT (intima-medial thickness) at 210 degrees',
'Mean carotid IMT (intima-medial thickness) at 210 degrees',
'Maximum carotid IMT (intima-medial thickness) at 210 degrees',
'Minimum carotid IMT (intima-medial thickness) at 240 degrees',
'Mean carotid IMT (intima-medial thickness) at 240 degrees',
'Maximum carotid IMT (intima-medial thickness) at 240 degrees'],
27: ['H25 Senile cataract',
'H26 Other cataract',
'N83 Noninflammatory disorders of ovary, Fallopian tube and broad ligament',
'Other retinal disorders',
'Glaucoma',
'Cataract',
'Senile cataract',
'Other disorders of eye',
'Aphakia and other disorders of lens',
'Noninflammatory female genital disorders',
'Noninflammatory disorders of ovary, fallopian tube, and broad ligament',
'Endometrial hyperplasia',
'Hypertrophy of female genital organs',
'Ovarian cyst',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported'],
28: ['Systolic blood pressure, manual reading',
'Diastolic blood pressure, manual reading',
'Diastolic blood pressure, manual reading, adjusted by medication',
'Mean arterial pressure, manual reading',
'Mean arterial pressure, manual reading, adjusted by medication',
'Pulse pressure, manual reading',
'Pulse pressure, manual reading, adjusted by medication',
'Systolic blood pressure, manual reading, adjusted by medication'],
29: ['E03 Other hypothyroidism',
'Hypothyroidism',
'Hypothyroidism NOS',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code',
'Treatment/medication code'],
30: [],
31: ['Treatment/medication code'],
32: [],
33: ['H52 Disorders of refraction and accommodation',
'Myopia',
'Frequency of urination and polyuria'],
34: ['K57 Diverticular disease of intestine',
'K62 Other diseases of anus and rectum',
'K63 Other diseases of intestine',
'Benign neoplasm of colon',
'Diverticulosis and diverticulitis',
'Diverticulosis',
'Anal and rectal conditions',
'Anal and rectal polyp',
'Other disorders of intestine'],
35: [],
36: ['Intra-ocular pressure, Goldmann-correlated (right)',
'Corneal resistance factor (right)',
'Intra-ocular pressure, Goldmann-correlated (left)',
'Corneal resistance factor (left)'],
37: [],
38: ['I26 Pulmonary embolism',
'I80 Phlebitis and thrombophlebitis',
'Pulmonary heart disease',
'Acute pulmonary heart disease',
'Pulmonary embolism and infarction, acute',
'Phlebitis and thrombophlebitis',
'Phlebitis and thrombophlebitis of lower extremities',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported'],
39: ['COVID-19 positive (controls include untested)',
'COVID-19 positive (controls include untested)',
'COVID-19 positive (controls include untested), only patients from centers in England',
'COVID-19 positive (controls include untested), only patients from centers in England',
'COVID-19 positive (controls only COVID-19 negative)',
'COVID-19 positive (controls only COVID-19 negative)'],
40: ['K80 Cholelithiasis',
'K82 Other diseases of gallbladder',
'K83 Other diseases of biliary tract',
'Jaundice (not of newborn)',
'Abnormal results of function study of liver',
'Cholelithiasis and cholecystitis',
'Cholelithiasis',
'Cholelithiasis with acute cholecystitis',
'Cholelithiasis with other cholecystitis',
'Calculus of bile duct',
'Cholecystitis without cholelithiasis',
'Other biliary tract disease',
'Obstruction of bile duct',
'Other disorders of gallbladder',
'Other disorders of biliary tract',
'Non-cancer illness code, self-reported'],
41: ['N13 Obstructive and reflux uropathy',
'N32 Other disorders of bladder',
'N39 Other disorders of urinary system',
'Z46 Fitting and adjustment of other devices',
'Cancer of urinary organs (incl. kidney and bladder)',
'Cancer of bladder',
'Other disorders of the kidney and ureters',
'Stricture/obstruction of ureter',
'Pyelonephritis',
'Urinary tract infection',
'Cystitis and urethritis',
'Cystitis',
'Chronic cystitis',
'Hematuria',
'Hydronephrosis',
'Other disorders of bladder',
'Bladder neck obstruction',
'Other disorders of urethra and urinary tract',
'Urethral stricture (not specified as infectious)',
'Other symptoms/disorders or the urinary system',
'Urinary obstruction',
'Retention of urine',
'Urinary incontinence',
'Other abnormality of urination',
'Hyperplasia of prostate'],
42: ['C44 Other malignant neoplasms of skin',
'L57 Skin changes due to chronic exposure to nonionising radiation',
'Skin cancer',
'Other non-epithelial cancer of skin',
'Degenerative skin conditions and other dermatoses',
'Actinic keratosis',
'Dermatitis due to solar radiation',
'Chronic dermatitis due to solar radiation'],
43: ['I35 Nonrheumatic aortic valve disorders',
'Rheumatic disease of the heart valves',
'Aortic valve disease',
'Heart valve disorders',
'Nonrheumatic aortic valve disorders',
'Heart valve replaced',
'Cardiac and circulatory congenital anomalies',
'Cardiac congenital anomalies',
'Congenital anomalies of great vessels',
'Duration screen displayed'],
44: [],
45: ['Treatment/medication code',
'Interpolated Year when non-cancer illness first diagnosed',
'Interpolated Age of participant when non-cancer illness first diagnosed',
'Age hay fever, rhinitis or eczema diagnosed',
'Age asthma diagnosed'],
46: ['G81 Hemiplegia',
'I63 Cerebral infarction',
'I67 Other cerebrovascular diseases',
'I69 Sequelae of cerebrovascular disease',
'R47 Speech disturbances, not elsewhere classified',
'T39 Poisoning by nonopioid analgesics, antipyretics and antirheumatics',
'T42 Poisoning by antiepileptic, sedative-hypnotic and anti-Parkinsonism drugs',
'T43 Poisoning by psychotropic drugs, not elsewhere classified',
'T51 Toxic effect of alcohol',
'X60 Intentional self-poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics',
'X61 Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, anti-Parkinsonism and psychotropic drugs, not elsewhere classified',
'Aphasia/speech disturbance',
'Suicidal ideation or attempt',
'Suicide or self-inflicted injury',
'Hemiplegia',
'Cerebrovascular disease',
'Occlusion of cerebral arteries',
'Cerebral artery occlusion, with cerebral infarction',
'Cerebral ischemia',
'Late effects of cerebrovascular disease',
'Poisoning by psychotropic agents',
'Toxic effect of (non-ethyl) alcohol and petroleum and other solvents'],
47: ['F10 Mental and behavioural disorders due to use of alcohol',
'Substance addiction and disorders',
'Alcohol-related disorders',
'Sweet pepper intake'],
48: [],
49: [],
50: ['Astigmatism angle (right)',
'Astigmatism angle (left)',
'3mm weak meridian angle (right)',
'6mm weak meridian angle (right)',
'6mm weak meridian angle (left)',
'3mm weak meridian angle (left)',
'3mm strong meridian angle (left)',
'6mm strong meridian angle (left)',
'6mm strong meridian angle (right)',
'3mm strong meridian angle (right)',
'3mm cylindrical power angle (left)',
'6mm cylindrical power angle (left)',
'6mm cylindrical power angle (right)',
'3mm cylindrical power angle (right)'],
51: ['I42 Cardiomyopathy',
'Cardiomyopathy',
'Primary/intrinsic cardiomyopathies'],
52: ['C18 Malignant neoplasm of colon',
'Colorectal cancer',
'Colon cancer',
'Malignant neoplasm of rectum, rectosigmoid junction, and anus',
'Cancer code, self-reported',
'Age diabetes diagnosed'],
53: ['Anterior thigh lean muscle volume (right)',
'Posterior thigh lean muscle volume (right)',
'Anterior thigh lean muscle volume (left)',
'Posterior thigh lean muscle volume (left)',
'Visceral adipose tissue volume (VAT)',
'Abdominal subcutaneous adipose tissue volume (ASAT)',
'Total thigh muscle volume',
'Total trunk fat volume'],
54: ['G55 Nerve root and plexus compressions in diseases classified elsewhere',
"K50 Crohn's disease [regional enteritis]",
'K51 Ulcerative colitis',
'M48 Other spondylopathies',
'M50 Cervical disk disorders',
'M51 Other intervertebral disk disorders',
'Nerve root and plexus disorders',
'Inflammatory bowel disease and other gastroenteritis and colitis',
'Regional enteritis',
'Ulcerative colitis',
'Spinal stenosis',
'Intervertebral disc disorders',
'Degeneration of intervertebral disc',
'Other and unspecified disc disorder',
'Sciatica',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported'],
55: ['O36 Maternal care for other known or suspected foetal problems',
'O63 Long labour',
'O68 Labour and delivery complicated by foetal stress [distress]',
'O70 Perineal laceration during delivery',
'O99 Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium',
'Hemorrhage during pregnancy; childbirth and postpartum',
'Early or threatened labor; hemorrhage in early pregnancy',
'Other complications of pregnancy NEC',
'Problems associated with amniotic cavity and membranes',
'Known or suspected fetal abnormality affecting management of mother',
'Fetal distress and abnormal forces of labor',
'Obstetrical/birth trauma',
'Complications of labor and delivery NEC'],
56: ['N81 Female genital prolapse',
'Genital prolapse',
'Prolapse of vaginal walls',
'stress incontinence, female'],
57: ['Other diseases of lung'],
58: [],
59: ['D51 Vitamin B12 deficiency anaemia',
'Other deficiency anemia',
'Megaloblastic anemia',
'Other vitamin B12 deficiency anemia',
'Non-cancer illness code, self-reported',
'ECG, phase time'],
60: [],
61: [],
62: [],
63: ['I73 Other peripheral vascular diseases',
'I74 Arterial embolism and thrombosis',
'I77 Other disorders of arteries and arterioles',
'Peripheral vascular disease',
'Peripheral vascular disease, unspecified',
'Arterial embolism and thrombosis',
'Stricture of artery',
'Intra-ocular pressure, corneal-compensated (right)',
'Corneal hysteresis (right)',
'Intra-ocular pressure, corneal-compensated (left)',
'Corneal hysteresis (left)'],
64: ['Uterine/Uterovaginal prolapse'],
65: ['M72 Fibroblastic disorders',
'Atherosclerosis',
'Atherosclerosis of the extremities',
'Disorders of muscle, ligament, and fascia',
'Fasciitis',
"Contracture of palmar fascia [Dupuytren's disease]"],
66: ['C67 Malignant neoplasm of bladder',
'N20 Calculus of kidney and ureter',
'Malignant neoplasm of bladder',
'Urinary calculus',
'Calculus of kidney',
'Calculus of ureter',
'Renal colic',
'Non-cancer illness code, self-reported'],
67: ['Mean platelet (thrombocyte) volume'],
68: ['C34 Malignant neoplasm of bronchus and lung',
'Cancer of bronchus; lung'],
69: [],
70: ['K02 Dental caries',
'K04 Diseases of pulp and periapical tissues',
'Diseases of hard tissues of teeth',
'Dental caries',
'Diseases of pulp and periapical tissues',
'Periapical abscess',
'Gingival and periodontal diseases',
'Periodontitis (acute or chronic)',
'Chronic periodontitis'],
71: ['N95 Menopausal and other perimenopausal disorders',
'Mucous polyp of cervix',
'Menopausal and postmenopausal disorders',
'Postmenopausal bleeding',
'Years since last cervical smear test'],
72: ['Other disorders of arteries and arterioles'],
73: ['D50 Iron deficiency anaemia',
'L72 Follicular cysts of skin and subcutaneous tissue',
'Iron deficiency anemias',
'Iron deficiency anemias, unspecified or not due to blood loss',
'Diseases of hair and hair follicles',
'Diseases of sebaceous glands',
'Sebaceous cyst'],
74: ['Disorders of parathyroid gland'],
75: [],
76: ['K35 Acute appendicitis',
'Appendiceal conditions',
'Appendicitis',
'Acute appendicitis'],
77: ['G47 Sleep disorders',
'L40 Psoriasis',
'Sleep disorders',
'Sleep apnea',
'Psoriasis and related disorders',
'Psoriasis',
'Non-cancer illness code, self-reported',
'Non-cancer illness code, self-reported'],
78: ['R04 Haemorrhage from respiratory passages',
'Epistaxis or throat hemorrhage',
'Abnormal sputum',
'Hemoptysis'],
79: ['M20 Acquired deformities of fingers and toes',
'Acquired foot deformities',
'Acquired toe deformities',
'Hammer toe (acquired)',
'Hallux rigidus',
'Hallux valgus (Bunion)'],
80: ['N84 Polyp of female genital tract',
'Polyp of female genital organs',
'Polyp of corpus uteri'],
81: ['N41 Inflammatory diseases of prostate',
'Symptoms involving head and neck',
'Inflammatory diseases of prostate',
'Prostatitis',
'Chronic prostatitis'],
82: ['Hyposmolality and/or hyponatremia',
'Open wound or laceration of eye or eyelid'],
83: ['K76 Other diseases of liver',
'Chronic liver disease and cirrhosis',
'Other chronic nonalcoholic liver disease',
'Other disorders of liver'],
84: [],
85: ['H33 Retinal detachments and breaks',
'H40 Glaucoma',
'Retinal detachments and defects',
'Retinal detachment with retinal defect'],
86: ['I46 Cardiac arrest',
'Cardiac arrest and ventricular fibrillation',
'Cardiac arrest'],
87: ["C83 Diffuse non-Hodgkin's lymphoma",
"C85 Other and unspecified types of non-Hodgkin's lymphoma",
'Cancer within the respiratory system',
'Cancer of other lymphoid, histiocytic tissue',
'Non-Hodgkins lymphoma'],
88: ['K40 Inguinal hernia', 'Inguinal hernia'],
89: ['I12 Hypertensive renal disease',
'Hypertensive heart and/or renal disease',
'Hypertensive chronic kidney disease'],
90: ['K90 Intestinal malabsorption',
'Intestinal malabsorption (non-celiac)',
'Celiac disease',
'Non-cancer illness code, self-reported'],
91: ['I83 Varicose veins of lower extremities',
'Varicose veins',
'Varicose veins of lower extremity'],
92: ['I71 Aortic aneurysm and dissection',
'R06 Abnormalities of breathing',
'Other aneurysm',
'Aortic aneurysm',
'Abdominal aortic aneurysm',
'Respiratory abnormalities'],
93: [],
94: [],
95: [],
96: ['Cylindrical power (left)',
'6mm cylindrical power (left)',
'3mm cylindrical power (left)'],
97: ['E21 Hyperparathyroidism and other disorders of parathyroid gland',
'Hyperparathyroidism'],
98: [],
99: ['I44 Atrioventricular and left bundle-branch block',
'I45 Other conduction disorders',
'Cardiac conduction disorders',
'Atrioventricular [AV] block',
'First degree AV block',
'Bundle branch block',
'Left bundle branch block'],
100: ['K25 Gastric ulcer',
'Peptic ulcer (excl. esophageal)',
'Gastric ulcer',
'Duodenal ulcer'],
101: [],
102: ['D68 Other coagulation defects',
'Coagulation defects',
'Defibrination syndrome'],
103: [],
104: ['E16 Other disorders of pancreatic internal secretion',
'Other disorders of pancreatic internal secretion',
'Hypoglycemia'],
105: ['F41 Other anxiety disorders',
'N30 Cystitis',
'Anxiety disorders',
'Anxiety disorder'],
106: ['R22 Localised swelling, mass and lump of skin and subcutaneous tissue',
'Swelling, mass, or lump in head and neck [Space-occupying lesion, intracranial NOS]',
'Shortness of breath',
'Symptoms affecting skin',
'Localized superficial swelling, mass, or lump',
'Musculoskeletal symptoms referable to limbs'],
107: ['H65 Nonsuppurative otitis media',
'J33 Nasal polyp',
'Otitis media and Eustachian tube disorders',
'Otitis media',
'Nasal polyps',
'Interpolated Year when operation took place',
'Interpolated Age of participant when operation took place',
'Speech-reception-threshold (SRT) estimate (left)',
'Speech-reception-threshold (SRT) estimate (right)',
'Signal-to-noise-ratio (SNR) of triplet (left)',
'Mean signal-to-noise ratio (SNR), (left)',
'Signal-to-noise-ratio (SNR) of triplet (right)',
'Mean signal-to-noise ratio (SNR), (right)',
'Operation year/age first occurred'],
108: ['I95 Hypotension',
'Hypotension',
'Orthostatic hypotension',
'Hypotension NOS'],
109: ['I47 Paroxysmal tachycardia',
'Paroxysmal tachycardia, unspecified',
'Paroxysmal supraventricular tachycardia'],
110: ['K92 Other diseases of digestive system',
'Gastrointestinal hemorrhage',
'Hemorrhage of rectum and anus',
'Hemorrhage of gastrointestinal tract'],
111: [],
112: ['Other intestinal obstruction'],
113: ['H35 Other retinal disorders',
'Degeneration of macula and posterior pole of retina',
'Macular degeneration (senile) of retina NOS'],
114: ['Cylindrical power (right)',
'3mm cylindrical power (right)',
'6mm cylindrical power (right)'],
115: ['Pneumococcal pneumonia', 'Beer/cider intake'],
116: ['H72 Perforation of tympanic membrane',
'H90 Conductive and sensorineural hearing loss',
'Other disorders of tympanic membrane',
'Perforation of tympanic membrane',
'Monocyte percentage'],
117: ['K66 Other disorders of peritoneum',
'M10 Gout',
'Gout and other crystal arthropathies',
'Gout',
'Other disorders of peritoneum',
'Peritoneal adhesions (postoperative) (postinfection)'],
118: ['R26 Abnormalities of gait and mobility',
'Abnormal movement',
'Abnormality of gait'],
119: ['D69 Purpura and other haemorrhagic conditions',
'Purpura and other hemorrhagic conditions',
'Thrombocytopenia',
'Agorophobia, social phobia, and panic disorder'],
120: ['K85 Acute pancreatitis',
'K86 Other diseases of pancreas',
'Diseases of pancreas',
'Acute pancreatitis'],
121: ['Open-angle glaucoma', 'Primary open angle glaucoma'],
122: ['Ptosis of eyelid'],
123: [],
124: [],
125: ['H02 Other disorders of eyelid',
'H04 Disorders of lachrymal system',
'N43 Hydrocele and spermatocele',
'Other disorders of eyelids',
'Ectropion or entropion',
'Disorders of lacrimal system',
'Epiphora',
'Other disorders of testis',
'Hydrocele'],
126: ['D17 Benign lipomatous neoplasm',
'Lipoma',
'Lipoma of skin and subcutaneous tissue'],
127: [],
128: [],
129: [],
130: ['H54 Blindness and low vision',
'Disorders of refraction and accommodation; blindness and low vision',
'Blindness and low vision'],
131: [],
132: ['N87 Dysplasia of cervix uteri',
'Cervical cancer and dysplasia',
'Cervical intraepithelial neoplasia [CIN] [Cervical dysplasia]'],
133: ['G40 Epilepsy', 'Epilepsy'],
134: ['G45 Transient cerebral ischaemic attacks and related syndromes',
'M06 Other rheumatoid arthritis',
'Transient cerebral ischemia',
'Rheumatoid arthritis and other inflammatory polyarthropathies',
'Rheumatoid arthritis',
'Non-cancer illness code, self-reported',
'Treatment/medication code',
'Treatment/medication code'],
135: ['L03 Cellulitis',
'Superficial cellulitis and abscess',
'Cellulitis and abscess of arm/hand',
'Non-cancer illness code, self-reported'],
136: [],
137: ['K56 Paralytic ileus and intestinal obstruction without hernia',
'Intestinal obstruction without mention of hernia',
'Peritoneal or intestinal adhesions'],
138: ['L89 Decubitus ulcer',
'R00 Abnormalities of heart beat',
'Abnormal heart sounds',
'Tachycardia NOS',
'Palpitations',
'Chronic ulcer of skin',
'Decubitus ulcer'],
139: [],
140: ['Round of numeric memory test',
'Number of rounds of numeric memory test performed'],
141: [],
142: ['E53 Deficiency of other B group vitamins',
'Cancer of other female genital organs',
'Malignant neoplasm of ovary and other uterine adnexa',
'Malignant neoplasm of ovary',
'Vitamin deficiency',
'Vitamin B-complex deficiencies'],
143: ['F31 Bipolar affective disorder',
'Mood disorders',
'Bipolar',
'Non-cancer illness code, self-reported'],
144: ['I61 Intracerebral haemorrhage',
'Intracranial hemorrhage',
'Intracerebral hemorrhage'],
145: [],
146: [],
147: ['E83 Disorders of mineral metabolism',
'R56 Convulsions, not elsewhere classified',
'Disorders of mineral metabolism',
'Disorders of calcium/phosphorus metabolism',
'Epilepsy, recurrent seizures, convulsions',
'Convulsions',
'Dislocation'],
148: ['M16 Coxarthrosis [arthrosis of hip]'],
149: ['K01 Embedded and impacted teeth',
'Disorders of tooth development',
'Disturbances in tooth eruption'],
150: [],
151: ['R49 Voice disturbances',
'Diseases of the larynx and vocal cords',
'Voice disturbance',
'Mean time to correctly identify matches',
'Duration to first press of snap-button in each round'],
152: [],
153: [],
154: ['Acid-base balance disorder', 'Acidosis', 'Open wound of ear'],
155: ['N60 Benign mammary dysplasia',
'Benign mammary dysplasias',
'Other specified benign mammary dysplasias'],
156: ['G51 Facial nerve disorders',
'Disorders of other cranial nerves',
'Facial nerve disorders [CN7]'],
157: [],
158: [],
159: [],
160: ['H50 Other strabismus',
'Strabismus and other disorders of binocular eye movements',
'Strabismus (not specified as paralytic)'],
161: [],
162: ['Pulse wave Arterial Stiffness index', 'Pulse wave reflection index'],
163: [],
164: [],
165: [],
166: [],
167: ['R41 Other symptoms and signs involving cognitive functions and awareness',
'Neurological disorders',
'Altered mental status',
'Interpolated Year when cancer first diagnosed',
'Interpolated Age of participant when cancer first diagnosed',
'Cancer year/age first occurred'],
168: [],
169: ['Number of cigarettes previously smoked daily',
'Number of cigarettes smoked daily, combined previous and current smoking'],
170: ['Poisoning by antibiotics', 'Allergy/adverse effect of penicillin'],
171: [],
172: ['L60 Nail disorders', 'Diseases of nail, NOS', 'Ingrowing nail'],
173: ['Alcoholism'],
174: ['N31 Neuromuscular dysfunction of bladder, not elsewhere classified',
'N35 Urethral stricture',
'O80 Single spontaneous delivery',
'Intestinal infection',
'Functional disorders of bladder',
'Normal delivery'],
175: ['N73 Other female pelvic inflammatory diseases',
'Inflammatory diseases of female pelvic organs',
'Pelvic peritoneal adhesions, female (postoperative) (postinfection)'],
176: [],
177: [],
178: [],
179: [],
180: ['F05 Delirium, not induced by alcohol and other psychoactive substances',
'J35 Chronic diseases of tonsils and adenoids',
'Delirium dementia and amnestic and other cognitive disorders',
'Delirium due to conditions classified elsewhere',
'Acute and chronic tonsillitis',
'Chronic tonsillitis and adenoiditis'],
181: ['I34 Nonrheumatic mitral valve disorders',
'Nonrheumatic mitral valve disorders'],
182: ['Vitamin B12', 'Vitamin D'],
183: ['H00 Hordeolum and chalazion',
'Inflammation of the eye',
'Inflammation of eyelids'],
184: [],
185: ['J02 Acute pharyngitis',
'Acute upper respiratory infections of multiple or unspecified sites',
'Acute pharyngitis'],
186: [],
187: ['K42 Umbilical hernia', 'Umbilical hernia'],
188: ['Cancer of kidney and renal pelvis',
'Malignant neoplasm of kidney, except pelvis'],
189: [],
190: ['M67 Other disorders of synovium and tendon'],
191: [],
192: ['N42 Other disorders of prostate',
'R79 Other abnormal findings of blood chemistry',
'Other disorders of prostate',
'Other abnormal blood chemistry'],
193: [],
194: ['L90 Atrophic disorders of skin',
'Other hypertrophic and atrophic conditions of skin',
'Scar conditions and fibrosis of skin'],
195: [],
196: [],
197: ['I24 Other acute ischaemic heart diseases',
'Other acute and subacute forms of ischemic heart disease'],
198: [],
199: ['Other disorders of synovium, tendon, and bursa'],
200: ['S01 Open wound of head',
'Z83 Family history of other specific disorders',
'Streptococcus infection',
'Family history',
'Other open wound of head and face'],
201: ['H43 Disorders of vitreous body', 'Disorders of vitreous body'],
202: [],
203: [],
204: ['K55 Vascular disorders of intestine',
'Vascular insufficiency of intestine'],
205: [],
206: ['I31 Other diseases of pericardium', 'Carditis', 'Pericarditis'],
207: ['K14 Diseases of tongue',
'R30 Pain associated with micturition',
'Diseases and other conditions of the tongue',
'Dysuria'],
208: ['K58 Irritable bowel syndrome', 'Irritable Bowel Syndrome'],
209: ['A04 Other bacterial intestinal infections',
'A08 Viral and other specified intestinal infections',
'Bacterial enteritis',
'Viral Enteritis'],
210: ['R25 Abnormal involuntary movements', 'Abnormal involuntary movements'],
211: ['K08 Other disorders of teeth and supporting structures',
'R50 Fever of unknown origin',
'Other diseases of the teeth and supporting structures'],
212: [],
213: ["Raynaud's syndrome"],
214: [],
215: ['R20 Disturbances of skin sensation', 'Disturbance of skin sensation'],
216: [],
217: [],
218: [],
219: [],
220: ['R60 Oedema, not elsewhere classified', 'Edema'],
221: ['O02 Other abnormal products of conception',
'Miscarriage; stillbirth',
'Missed abortion/Hydatidiform mole'],
222: ['G43 Migraine',
'T83 Complications of genito-urinary prosthetic devices, implants and grafts',
'Migraine',
'Mechanical complication of unspecified genitourinary device, implant, and graft'],
223: ['J30 Vasomotor and allergic rhinitis', 'Allergic rhinitis'],
224: [],
225: [],
226: [],
227: [],
228: [],
229: [],
230: ['B37 Candidiasis', 'Candidiasis'],
231: [],
232: ['L02 Cutaneous abscess, furuncle and carbuncle',
'T82 Complications of cardiac and vascular prosthetic devices, implants and grafts',
'Carbuncle and furuncle',
'Complications of cardiac/vascular device, implant, and graft'],
233: ['J43 Emphysema',
'K11 Diseases of salivary glands',
'Emphysema',
'Diseases of the salivary glands'],
234: ['D18 Haemangioma and lymphangioma, any site',
'Hemangioma and lymphangioma, any site'],
235: ['K81 Cholecystitis',
'Abnormal findings on mammogram or breast exam',
'Lump or mass in breast'],
236: [],
237: [],
238: [],
239: [],
240: ['I84 Haemorrhoids', 'Hemorrhoids'],
241: ['N48 Other disorders of penis',
'Disorders of penis',
'Redundant prepuce and phimosis/BXO'],
242: [],
243: [],
244: ['N89 Other noninflammatory disorders of vagina',
'Noninflammatory disorders of vagina'],
245: ['E05 Thyrotoxicosis [hyperthyroidism]',
'E89 Postprocedural endocrine and metabolic disorders, not elsewhere classified',
'Thyrotoxicosis with or without goiter',
'Secondary hypothyroidism',
'Open wounds of extremities'],
246: [],
247: [],
248: ['Fried potatoes intake',
'Believed safe to perform brain MRI scan',
'Believed safe to perform abdominal MRI scan'],
249: ['D35 Benign neoplasm of other and unspecified endocrine glands',
'Benign neoplasm of other endocrine glands and related structures'],
250: ['N28 Other disorders of kidney and ureter, not elsewhere classified',
'Cyst of kidney, acquired'],
251: ['H61 Other disorders of external ear', 'Disorders of external ear'],
252: ['C43 Malignant melanoma of skin', 'Melanomas of skin, dx or hx'],
253: [],
254: ['C54 Malignant neoplasm of corpus uteri',
'Malignant neoplasm of uterus'],
255: [],
256: ['Fever of unknown origin'],
257: [],
258: ['D37 Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs',
'Neoplasm of unspecified nature of digestive system'],
259: [],
260: [],
261: [],
262: [],
263: [],
264: [],
265: ['Peripheral enthesopathies and allied syndromes'],
266: ['Frequency of inability to cease drinking in last year'],
267: ['Sliced bread intake', 'Number of bread slices with butter/margarine'],
268: ['K26 Duodenal ulcer'],
269: ['K43 Ventral hernia', 'Ventral hernia'],
270: [],
271: ['Visual disturbances'],
272: [],
273: ['N50 Other disorders of male genital organs',
'Other disorders of male genital organs'],
274: ['Ganglion and cyst of synovium, tendon, and bursa'],
275: [],
276: [],
277: ['J31 Chronic rhinitis, nasopharyngitis and pharyngitis',
'J96 Respiratory failure, not elsewhere classified',
'Chronic pharyngitis and nasopharyngitis',
'Respiratory insufficiency'],
278: ['Frequency of inability to stop worrying during worst period of anxiety'],
279: [],
280: [],
281: ['L08 Other local infections of skin and subcutaneous tissue'],
282: ['K70 Alcoholic liver disease',
'R59 Enlarged lymph nodes',
'Lymphadenitis',
'Alcoholic liver damage'],
283: ['D22 Melanocytic naevi'],
284: [],
285: ['N80 Endometriosis', 'Endometriosis'],
286: [],
287: ['K52 Other non-infective gastro-enteritis and colitis',
'Noninfectious gastroenteritis'],
288: [],
289: ['K65 Peritonitis',
'Right bundle branch block',
'Peritonitis and retroperitoneal infections'],
290: [],
291: ['Other diseases of respiratory system, not elsewhere classified',
'Other diseases of respiratory system, NEC'],
292: ['Illnesses of father'],
293: [],
294: [],
295: ['J84 Other interstitial pulmonary diseases',
'R63 Symptoms and signs concerning food and fluid intake',
'Symptoms concerning nutrition, metabolism, and development',
'Postinflammatory pulmonary fibrosis'],
296: [],
297: ['Derangement of joint, non-traumatic',
'Other derangement of joint',
'Fracture of neck of femur'],
298: [],
299: [],
300: ['I08 Multiple valve diseases',
'J98 Other respiratory disorders',
'Mitral valve disease'],
301: [],
302: ['H53 Visual disturbances'],
303: ['Pulmonary collapse; interstitial and compensatory emphysema'],
304: [],
305: [],
306: ['Other local infections of skin and subcutaneous tissue'],
307: ['H91 Other hearing loss', 'Hearing loss'],
308: [],
309: ['D23 Other benign neoplasms of skin', 'Benign neoplasm of skin'],
310: [],
311: [],
312: [],
313: [],
314: [],
315: [],
316: ['Traffic intensity on the nearest major road'],
317: ['Placenta previa and abruptio placenta', 'Acquired spondylolisthesis'],
318: ['R39 Other symptoms and signs involving the urinary system',
'Abnormal findings on examination of urine'],
319: ['M35 Other systemic involvement of connective tissue',
'Polymyalgia Rheumatica'],
320: ['L98 Other disorders of skin and subcutaneous tissue, not elsewhere classified',
'Disorder of skin and subcutaneous tissue NOS',
'Bread roll intake',
'Number of bread rolls with butter/margarine'],
321: [],
322: [],
323: [],
324: [],
325: [],
326: ['B95 Streptococcus and staphylococcus as the cause of diseases classified to other chapters',
'Illnesses of mother'],
327: ['K13 Other diseases of lip and oral mucosa',
'Other acquired musculoskeletal deformity'],
328: ['Curvature of spine', 'Kyphoscoliosis and scoliosis'],
329: [],
330: ['J32 Chronic sinusitis', 'Chronic sinusitis'],
331: ['N94 Pain and other conditions associated with female genital organs and menstrual cycle',
'Pain and other symptoms associated with female genital organs',
'Dyspareunia'],
332: ['R19 Other symptoms and signs involving the digestive system and abdomen',
'Symptoms involving digestive system'],
333: [],
334: ['Diseases of the oral soft tissues, excluding lesions specific for gingiva and tongue'],
335: [],
336: ['Inflammatory disease of cervix, vagina, and vulva',
'Cervicitis and endocervicitis'],
337: ['L30 Other dermatitis',
'Atopic/contact dermatitis due to other or unspecified'],
338: [],
339: ['H81 Disorders of vestibular function',
'Vertiginous syndromes and other disorders of vestibular system'],
340: [],
341: ['Number of cigarettes currently smoked daily (current cigarette smokers)',
'Difficulty not smoking for 1 day'],
342: [],
343: [],
344: ['3mm asymmetry angle (right)',
'6mm asymmetry angle (left)',
'3mm asymmetry angle (left)',
'6mm asymmetry index (left)'],
345: [],
346: [],
347: [],
348: [],
349: ['G62 Other polyneuropathies', 'Inflammatory and toxic neuropathy'],
350: [],
351: ['J34 Other disorders of nose and nasal sinuses',
'J93 Pneumothorax',
'Septal Deviations/Turbinate Hypertrophy',
'Other upper respiratory disease',
'Empyema and pneumothorax'],
352: ['Number of jobs held'],
353: ['Baguette intake', 'Number of baguettes with butter/margarine'],
354: [],
355: ['A09 Diarrhoea and gastro-enteritis of presumed infectious origin'],
356: ['T85 Complications of other internal prosthetic devices, implants and grafts'],
357: ['I65 Occlusion and stenosis of precerebral arteries, not resulting in cerebral infarction',
'Occlusion and stenosis of precerebral arteries',
'Seborrheic keratosis'],
358: ['Number of triplets attempted (left)',
'Number of triplets attempted (right)'],
359: ['Multiple sclerosis', 'Non-cancer illness code, self-reported'],
360: ['E04 Other non-toxic goitre', 'Nontoxic nodular goiter'],
361: [],
362: [],
363: [],
364: [],
365: [],
366: [],
367: ['M65 Synovitis and tenosynovitis', 'Synovitis and tenosynovitis'],
368: ['M70 Soft tissue disorders related to use, overuse and pressure',
'Bursitis',
'Other disorders of soft tissues',
'Rheumatism, unspecified and fibrositis'],
369: [],
370: [],
371: ['R03 Abnormal blood-pressure reading, without diagnosis',
'Elevated blood pressure reading without diagnosis of hypertension'],
372: [],
373: ['N64 Other disorders of breast',
'Other nonmalignant breast conditions'],
374: [],
375: [],
376: [],
377: [],
378: [],
379: [],
380: ['S61 Open wound of wrist and hand',
'S66 Injury of muscle and tendon at wrist and hand level'],
381: ['N90 Other noninflammatory disorders of vulva and perineum',
'Noninflammatory disorders of vulva and perineum'],
382: [],
383: [],
384: [],
385: ['B34 Viral infection of unspecified site', 'Viral infection'],
386: [],
387: [],
388: ['G99 Other disorders of nervous system in diseases classified elsewhere',
'Degenerative disease of the spinal cord'],
389: [],
390: ['O42 Premature rupture of membranes'],
391: ['O26 Maternal care for other conditions predominantly related to pregnancy'],
392: [],
393: [],
394: ['R93 Abnormal findings on diagnostic imaging of other body structures',
'Abnormal findings on exam of gastrointestinal tract/ abdominal area'],
395: ['Orchitis and epididymitis'],
396: [],
397: [],
398: ['Nephritis; nephrosis; renal sclerosis', 'Glomerulonephritis'],
399: [],
400: [],
401: ['Genitourinary congenital anomalies',
'Congenital anomalies of urinary system'],
402: ['Intake of artificial sweetener added to coffee'],
403: ['J38 Diseases of vocal cords and larynx, not elsewhere classified'],
404: [],
405: ['Vitamin D deficiency',
'6mm regularity index (left)',
'3mm regularity index (left)'],
406: [],
407: ['S00 Superficial injury of head',
'S80 Superficial injury of lower leg',
'Superficial injury without mention of infection',
'Contusion'],
408: ['Symptoms and disorders of the joints',
'Joint effusions',
'Crispbread intake',
'Number of crackers/crispbreads with butter/margarine'],
409: [],
410: ['Instant coffee intake'],
411: ['3mm regularity index (right)'],
412: [],
413: [],
414: [],
415: ['Non-cancer illness code, self-reported'],
416: [],
417: ['Benign neoplasm of breast'],
418: ['Other bread intake'],
419: [],
420: [],
421: [],
422: [],
423: ['Poultry intake'],
424: [],
425: [],
426: [],
427: [],
428: [],
429: [],
430: [],
431: [],
432: [],
433: [],
434: ['S82 Fracture of lower leg, including ankle',
'Fracture of tibia and fibula'],
435: [],
436: [],
437: [],
438: [],
439: [],
440: [],
441: [],
442: [],
443: [],
444: [],
445: [],
446: [],
447: ['Dementias'],
448: [],
449: ['I49 Other cardiac arrhythmias', 'Arrhythmia (cardiac) NOS'],
450: [],
451: [],
452: ['Subarachnoid hemorrhage'],
453: [],
454: [],
455: ['Effects of other external causes'],
456: [],
457: [],
458: [],
459: [],
460: [],
461: [],
462: ['Intake of artificial sweetener added to tea',
'Volume level set by participant (left)',
'Volume level set by participant (right)'],
463: [],
464: [],
465: [],
466: [],
467: [],
468: [],
469: [],
470: [],
471: [],
472: ['Other disorders of bone and cartilage'],
473: [],
474: [],
475: [],
476: ['R52 Pain, not elsewhere classified',
'Other symptoms',
'Malunion and nonunion of fracture'],
477: [],
478: [],
479: [],
480: [],
481: [],
482: [],
483: [],
484: [],
485: [],
486: [],
487: [],
488: [],
489: [],
490: [],
491: [],
492: [],
493: [],
494: [],
495: ['T78 Adverse effects, not elsewhere classified'],
496: [],
497: ['S09 Other and unspecified injuries of head', 'Injury, NOS'],
498: [],
499: [],
500: [],
501: [],
502: ['Retinal vascular changes and abnomalities'],
503: [],
504: [],
505: [],
506: [],
507: [],
508: [],
509: [],
510: [],
511: [],
512: ['R01 Cardiac murmurs and other cardiac sounds'],
513: [],
514: [],
515: [],
516: [],
517: [],
518: [],
519: [],
520: [],
521: [],
522: [],
523: [],
524: [],
525: [],
526: [],
527: [],
528: [],
529: [],
530: ['L91 Hypertrophic disorders of skin'],
531: [],
532: [],
533: [],
534: [],
535: [],
536: [],
537: [],
538: ['Number of night shifts worked monthly during mixed shift periods'],
539: [],
540: [],
541: [],
542: [],
543: [],
544: [],
545: [],
546: [],
547: [],
548: [],
549: [],
550: [],
551: [],
552: [],
553: [],
554: [],
555: [],
556: [],
557: [],
558: [],
559: [],
560: [],
561: [],
562: [],
563: [],
564: [],
565: [],
566: [],
567: [],
568: [],
569: [],
570: [],
571: [],
572: [],
573: [],
574: [],
575: [],
576: [],
577: [],
578: [],
579: [],
580: [],
581: [],
582: [],
583: [],
584: [],
585: [],
586: [],
587: [],
588: [],
589: [],
590: [],
591: [],
592: [],
593: [],
594: [],
595: [],
596: [],
597: [],
598: [],
599: [],
600: [],
601: [],
602: [],
603: [],
604: [],
605: [],
606: [],
607: [],
608: [],
609: [],
610: [],
611: [],
612: [],
613: [],
614: [],
615: [],
616: [],
617: [],
618: [],
619: [],
620: [],
621: [],
622: [],
623: [],
624: [],
625: [],
626: [],
627: [],
628: [],
629: [],
630: [],
631: [],
632: [],
633: [],
634: [],
635: [],
636: [],
637: [],
638: [],
639: [],
640: [],
641: [],
642: [],
643: [],
644: [],
645: [],
646: [],
647: [],
648: [],
649: [],
650: [],
651: [],
652: [],
653: [],
654: [],
655: [],
656: [],
657: [],
658: [],
659: [],
660: [],
661: [],
662: [],
663: [],
664: [],
665: [],
666: [],
667: [],
668: [],
669: [],
670: [],
671: [],
672: [],
673: [],
674: [],
675: [],
676: [],
677: [],
678: [],
679: [],
680: [],
681: [],
682: [],
683: [],
684: [],
685: [],
686: [],
687: [],
688: [],
689: [],
690: [],
691: [],
692: [],
693: [],
694: [],
695: [],
696: [],
697: [],
698: [],
699: [],
700: [],
701: [],
702: [],
703: [],
704: [],
705: [],
706: [],
707: [],
708: [],
709: [],
710: [],
711: [],
712: [],
713: [],
714: [],
715: [],
716: [],
717: [],
718: [],
719: [],
720: [],
721: [],
722: [],
723: [],
724: [],
725: [],
726: [],
727: [],
728: [],
729: [],
730: [],
731: [],
732: [],
733: [],
734: [],
735: [],
736: [],
737: [],
738: [],
739: [],
740: [],
741: [],
742: [],
743: [],
744: [],
745: [],
746: [],
747: [],
748: [],
749: [],
750: [],
751: [],
752: [],
753: [],
754: [],
755: [],
756: [],
757: [],
758: [],
759: [],
760: [],
761: [],
762: [],
763: [],
764: [],
765: [],
766: [],
767: [],
768: [],
769: [],
770: [],
771: [],
772: [],
773: [],
774: [],
775: [],
776: [],
777: [],
778: [],
779: [],
780: [],
781: [],
782: [],
783: [],
784: [],
785: [],
786: [],
787: [],
788: [],
789: [],
790: [],
791: [],
792: [],
793: [],
794: [],
795: [],
796: [],
797: [],
798: [],
799: [],
800: [],
801: [],
802: [],
803: [],
804: [],
805: [],
806: [],
807: [],
808: [],
809: [],
810: [],
811: [],
812: [],
813: [],
814: [],
815: [],
816: [],
817: [],
818: [],
819: [],
820: [],
821: [],
822: [],
823: [],
824: [],
825: [],
826: [],
827: [],
828: [],
829: [],
830: [],
831: [],
832: [],
833: [],
834: [],
835: [],
836: [],
837: [],
838: [],
839: [],
840: [],
841: [],
842: [],
843: [],
844: [],
845: [],
846: [],
847: [],
848: [],
849: [],
850: [],
851: [],
852: [],
853: [],
854: [],
855: [],
856: [],
857: [],
858: [],
859: [],
860: [],
861: [],
862: [],
863: [],
864: [],
865: [],
866: [],
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871: [],
872: [],
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875: [],
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888: [],
889: [],
890: [],
891: [],
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893: [],
894: [],
895: [],
896: [],
897: [],
898: [],
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900: [],
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...}import requests
import json
def get_opentarget_score(gene_id):
# Build query string to get association information
query_string = """
query TargetAssociationsQuery(
$ensemblId: String!
$filter: String
$sortBy: String!
$enableIndirect: Boolean!
) {
target(ensemblId: $ensemblId) {
id
approvedSymbol
associatedDiseases(
orderByScore: $sortBy
BFilter: $filter
enableIndirect: $enableIndirect
) {
count
rows {
disease {
id
name
}
score
}
}
}
}
"""
# Set variables object of arguments to be passed to endpoint
variables = {
"ensemblId": gene_id,
"filter": focal_disease["opentarget_name"],
"sortBy": "score",
"enableIndirect": False
}
# Set base URL of GraphQL API endpoint
base_url = "https://api.platform.opentargets.org/api/v4/graphql"
# print (gene_id)
# Perform POST request and check status code of response
r = requests.post(base_url, json={"query": query_string, "variables": variables})
# print(r.status_code)
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
# print(api_response)
score = 0.0
if api_response['data']['target'] is not None:
associated_diseases = api_response['data']['target']['associatedDiseases']['rows']
for d in associated_diseases:
if d['disease']['id'] == focal_disease["opentarget_id"]:
score = d['score']
# print(score)
return score
def get_variant_names(df):
vstr_list = list()
for i in range(df.shape[0]):
vstr = 'chr' + df.iloc[i][['chr', 'rsid', 'Gene_name']].astype('str').str.cat(sep=' | ')
gene_id = df.iloc[i]['ensembl_gene_id']
if not pd.isna(gene_id):
assoc_score = get_opentarget_score(gene_id)
vstr += f" | {assoc_score:.3f}"
else:
vstr += f" | NaN"
vstr_list.append(vstr)
return vstr_list
top_variant_names = get_variant_names(top_variant_df)fig = plt.figure(figsize = (8, 12))
ax1 = fig.add_subplot(111)
n_plot_variants = 20
xvals = top_variant_score[:n_plot_traits]
yvals = np.arange(n_plot_traits)[::-1]
ax1.barh(yvals, xvals, align = 'center', height = 0.7)
ax1.set_yticks(yvals)
ax1.set_yticklabels(top_variant_names[:n_plot_traits])
for side in ['top', 'right', 'left']:
ax1.spines[side].set_visible(False)
ax1.tick_params(left=False)
ax1.set_xlabel(f"Contribution of variants to PC{top_factor + 1}")
plt.show()
gene_id_array = variant_df['ensembl_gene_id'][~variant_df['ensembl_gene_id'].isna()].unique()
# all_assoc_scores = list()
# for gene_id in gene_id_array:
# # print(gene_id)
# all_assoc_scores.append(get_opentarget_score(gene_id))
# all_assoc_scores_arr = np.array(all_assoc_scores)
# np.save("/gpfs/commons/home/sbanerjee/work/npd/PanUKB/results/open_targets_triglycerides_assoc_scores_all_genes", all_assoc_scores_arr)
all_assoc_scores_arr = np.load("/gpfs/commons/home/sbanerjee/work/npd/PanUKB/results/open_targets_triglycerides_assoc_scores_all_genes.npy")fig = plt.figure(figsize = (8, 3))
ax1 = fig.add_subplot(111)
ax1.hist(all_assoc_scores_arr[all_assoc_scores_arr > 0.01], color = '#A6BDD7')
ax1.set_xlabel("Association Score")
ax1.set_ylabel("Number of genes")
plt.show()
all_assoc_scores_arr.shape(11546,)np.where(np.array(all_assoc_scores) > 0)[0].shape(1467,)all_assoc_scores_arr[all_assoc_scores_arr > 0.05].shape(1079,)