pqtls
Identifier
Section titled “Identifier”Description
Section titled “Description”Protein quantitative trait loci (pQTL) association results.
Primary results table (~65 billion rows).
Six proteins were included in multiple Olink panels.
The rest of the proteins were measured in a single panel.
One row per (ancestry, protein_id, panel, variant) pQTL association.
Always filter by protein_id AND ancestry (partition columns; panel is also a partition column and is required when a protein appears on multiple panels).
For proteins measured in multiple panels, make a distinction between results from each panel.
Sort by neg_log_10_p_value DESC for most significant hits.
Genome-wide significance threshold is ~7.3 (-log10(5e-8)).
To query by gene name: first get protein_id from assays table using gene_symbol, then query this table.
If no ancestry is specified, filter to the ALL ancestry partition and make a note in the response about the lack of a specific population.
To determine if a pQTL is cis or trans: 1. look up the gene_symbol in the genes table, 2. variants on the same chromosome as the gene and within approximately 1 Mb of the gene start_position or end_position are cis-pQTLs, 3. variants on a different chromosome, or on the same chromosome but far away (>1 Mb from start_position or end_position) are trans-pQTLs.
To find trans-pQTLs, query with chromosome != the gene chromosome to find cross-chromosome hits in a single query, then check the gene chromosome for hits >1 Mb away.
Related tables: ukb_ppp.assays (join on protein_id); ukb_ppp.variants (join on variant_id).
Partitions
Section titled “Partitions”ancestry'AFR''ALL''AMR''CSA''EAS''EUR''MID'
protein_id'A0FGR8''A1E959''A1KZ92''A1L4H1''A2VDF0''A4D1B5''A6BM72''A6NC86''A6NCE7''A6NDB9''A6NFN3''A6NGG8''A6NGN9''A6NHS7''A6NI73''A6NLU5''A6NM11''A7E2Y1''A8MTB9''A8MVW0''A8MVW5''A8MVZ5''A8MYV0''B0FP48''B1AKI9''B2RUY7''B6A8C7''B6SEH8''E2RYF7''I3L3R5''NTproBNP''O00148''O00161''O00175''O00182''O00186''O00194''O00203''O00206''O00214''O00220''O00221''O00233''O00241''O00244''O00253''O00273''O00291''O00292''O00300''O00308''O00327''O00337''O00339''O00391''O00399''O00401''O00422''O00425''O00451''O00468''O00533''O00534''O00548''O00559''O00567''O00584''O00585''O00592''O00602''O00622''O00626''O00748''O14503''O14523''O14530''O14558''O14578''O14579''O14594''O14618''O14625''O14662''O14713''O14717''O14737''O14745''O14763''O14773''O14786''O14788''O14791''O14793''O14798''O14828''O14836''O14841''O14867''O14879''O14904''O14917''O14933''O14944''O14958''O14960''O14964''O14967''O14974''O15013''O15018''O15020''O15031''O15078''O15083''O15116''O15117''O15123''O15164''O15169''O15182''O15197''O15211''O15212''O15213''O15232''O15234''O15240''O15263''O15264''O15269''O15294''O15305''O15335''O15350''O15354''O15357''O15382''O15389''O15394''O15400''O15444''O15455''O15467''O15496''O43155''O43184''O43186''O43240''O43247''O43278''O43280''O43290''O43291''O43312''O43320''O43396''O43399''O43405''O43422''O43423''O43432''O43464''O43474''O43493''O43504''O43505''O43508''O43521-2''O43524''O43557''O43561''O43570''O43583''O43597''O43598''O43639''O43653''O43663''O43665''O43681''O43699''O43707''O43715''O43734''O43736''O43739''O43752''O43768''O43776''O43805''O43827''O43854''O43866''O43889''O43895''O43896''O43903''O43915''O43927''O60218''O60220''O60232''O60234''O60235''O60237''O60238''O60240''O60242''O60243''O60245''O60259''O60279''O60437''O60447''O60449''O60462''O60469''O60476''O60496''O60500''O60502''O60542''O60575''O60603''O60609''O60635''O60662''O60664''O60701''O60749''O60760''O60763''O60825''O60828''O60869''O60880''O60884''O60890''O60907''O60911''O60934''O60939''O60941''O75015''O75023''O75054''O75061''O75071''O75077''O75121''O75144''O75146''O75154''O75167''O75173''O75190''O75223''O75293''O75312''O75326''O75330''O75339''O75340''O75347''O75348''O75351''O75354''O75356''O75365''O75380''O75409''O75427''O75460''O75462''O75475''O75493''O75506''O75509''O75521''O75528''O75534''O75563''O75569''O75592''O75594''O75629''O75631''O75665''O75688''O75695''O75711''O75718''O75781''O75787''O75791''O75792''O75794''O75830''O75843''O75882-2''O75888''O75940''O76036''O76038''O76039''O76061''O76070''O76074''O76076''O76096''O77932''O94760''O94766''O94779''O94813''O94830''O94856''O94903''O94907''O94916''O94979''O94985''O94986''O94988''O94992''O95049''O95157''O95166''O95180''O95183''O95196''O95202''O95256''O95274''O95295''O95372''O95379''O95388''O95393''O95407''O95429''O95433''O95445''O95466''O95467''O95497''O95498''O95502''O95544''O95630''O95633''O95644''O95670''O95684''O95696''O95715''O95721''O95727''O95750''O95760''O95777''O95786''O95793''O95817''O95825''O95831''O95835''O95841''O95858''O95866''O95954''O95965''O95971''O95980''O95988''O95994''O95997''O95998''O96007''O96013''O96017''P00167''P00325''P00352''P00390''P00441''P00519''P00533''P00568''P00734''P00736''P00740''P00742''P00746''P00747''P00748''P00749''P00750''P00751''P00797''P00813''P00915''P00918''P00966''P00995''P01008''P01009''P01011''P01019''P01024''P01031''P01033''P01034''P01037''P01100''P01112''P01127''P01130''P01133''P01135''P01137''P01138''P01178''P01189''P01210''P01215''P01222''P01225''P01229''P01236''P01241''P01242''P01258''P01266''P01270''P01275''P01298''P01303''P01350''P01374''P01375''P01579''P01583''P01584''P01588''P01589''P01591''P01730''P01732''P01833''P01903''P02008''P02144''P02452''P02458''P02461''P02462''P02533''P02647''P02649''P02652''P02654''P02671''P02730''P02743''P02745''P02748''P02749''P02750''P02751''P02760''P02763''P02765''P02766''P02771''P02774''P02775''P02776''P02778''P02786''P02787''P02818''P03372''P03950''P03951''P03952''P03956''P04040''P04054''P04062''P04066''P04070''P04080''P04083''P04085''P04090''P04114''P04118''P04141''P04155''P04179''P04180''P04183''P04196''P04216''P04217''P04233''P04234''P04275''P04278''P04406''P04439''P04626''P04637''P04746''P04792''P04808''P05000''P05026''P05060''P05067''P05089''P05090''P05091''P05107''P05112''P05113''P05121''P05154''P05155''P05156''P05160''P05164''P05187''P05231''P05305''P05362''P05412''P05413''P05451''P05452''P05455''P05543''P05546''P05549''P05556''P05783''P05787''P05937''P05976''P06127''P06132''P06213''P06276''P06280''P06396''P06401''P06493''P06681''P06727''P06729''P06730''P06731''P06733''P06734''P06744''P06748''P06753''P06756''P06850''P06858''P06870''P07093''P07098''P07108''P07148''P07196''P07204''P07225''P07237''P07288''P07306''P07307''P07311''P07320''P07332''P07333''P07339''P07355''P07358''P07359''P07451''P07478''P07492''P07585''P07602''P07711''P07741''P07766''P07858''P07911''P07942''P07947''P07948''P07949''P07954''P07992''P07998''P08069''P08118''P08134''P08138''P08174''P08185''P08217''P08236''P08254''P08263''P08294''P08319''P08397''P08473''P08519''P08571''P08575''P08579''P08581''P08582''P08590''P08603''P08648''P08651''P08670''P08697''P08700''P08709''P08727''P08758''P08833''P08887''P08908''P08913''P08962''P09038''P09093''P09104''P09105''P09110''P09172''P09211''P09237''P09238''P09326''P09341''P09382''P09417''P09455''P09466''P09467''P09486''P09496''P09525''P09529''P09543''P09564''P09601''P09603''P09619''P09668''P09681''P09683''P09693''P09758''P09769''P09871''P09874''P09914''P09919''P09923''P09958''P09960''P0C7L1''P0C7M8''P0C862''P0CG30''P0CG37''P0DJD7''P0DKB5''P0DML2''P0DMV8''P0DN86''P0DOY2''P0DPI2''P0DUB6_P0DTE7_P0DTE8''P10070''P10082''P10092''P10109''P10144''P10145''P10147''P10301''P10398''P10415''P10451''P10523''P10586''P10599''P10606''P10636''P10643''P10644''P10645''P10646''P10721''P10746''P10747''P10767''P10909''P10912''P11137''P11215''P11226''P11229''P11234''P11274''P11279''P11310''P11387''P11464''P11487''P11532''P11684''P11717''P12004''P12034''P12081''P12104''P12111''P12270''P12277''P12318''P12319''P12429''P12532''P12544''P12644''P12724''P12821''P12829''P12830''P12872''P12931''P12955''P13051''P13224''P13232''P13236''P13284''P13385''P13473''P13500''P13501''P13521''P13591''P13598''P13611''P13647''P13667''P13686''P13688''P13693''P13725''P13726''P13727''P13747''P13796''P13807''P13861''P13929''P13987''P13995''P14091''P14136''P14151''P14174''P14207''P14209''P14210''P14317''P14384''P14415''P14543''P14555''P14625''P14649''P14778''P14780''P14784''P14854''P14868''P14902''P15018''P15085''P15086''P15090''P15121''P15144''P15151''P15248''P15260''P15289''P15291''P15311''P15328''P15336''P15502''P15509''P15514''P15529''P15531''P15692''P15848''P15907''P15927''P16035''P16066''P16109''P16112''P16233''P16234''P16278''P16284''P16410''P16422''P16442''P16444''P16455''P16562''P16581''P16671''P16860''P16870''P16871''P17050''P17174''P17181''P17301''P17405''P17516''P17538''P17568''P17643''P17676''P17813''P17900''P17927''P17931''P17936''P17948''P17980''P18031''P18065''P18084''P18428''P18510''P18564''P18627''P18754''P18827''P18848''P19021''P19022''P19075''P19256''P19320''P19429''P19438''P19440''P19474''P19525''P19526''P19801''P19827''P19838''P19876''P19878''P19883''P19957''P19961''P19971''P20023''P20042''P20061''P20062''P20138''P20155''P20160''P20273''P20333''P20340''P20382''P20472''P20645''P20700''P20701''P20702''P20711''P20718''P20742''P20774''P20783''P20807''P20809''P20823''P20827''P20849''P20851''P20908''P20916''P20929''P20936''P21128''P21217_Q11128''P21246''P21549''P21579''P21583''P21589''P21673''P21695''P21709''P21741''P21754''P21757''P21781''P21802''P21810''P21817''P21854''P21860''P21912''P21964''P21980''P22004''P22033''P22079''P22102''P22105''P22223''P22301''P22303''P22304''P22307''P22455''P22466''P22528''P22676''P22692''P22748''P22749''P22894''P22897''P23141''P23229''P23276''P23280''P23284''P23327''P23381''P23435''P23467''P23471''P23511''P23515''P23526''P23560''P23582''P23588''P23634''P23743''P23771''P23919''P24001''P24071''P24158''P24386''P24387''P24394''P24530''P24592''P24666''P24821''P24864''P24928''P25092''P25116''P25391''P25440''P25445''P25490''P25685''P25686''P25774''P25786''P25815''P25942''P26010''P26022''P26378''P26436''P26440''P26441''P26447''P26639''P26715''P26718''P26842''P26927''P26951''P27169''P27348''P27352''P27487''P27540''P27695''P27701''P27918''P27930''P28222''P28325''P28799''P28827''P28838''P28845''P28906''P28907''P28908''P29017''P29218''P29279''P29317''P29350''P29353''P29377''P29459_P29460''P29460''P29466''P29474''P29475''P29536''P29622''P29692''P29965''P30039''P30040''P30041''P30043''P30044''P30046''P30047''P30048''P30049''P30084''P30086''P30101''P30203''P30260''P30279''P30304''P30405''P30419''P30519''P30530''P30533''P30613''P30740''P30838''P31146''P31350''P31371''P31431''P31483''P31689''P31751''P31785''P31948''P31949''P31994''P31997''P32004''P32119''P32241''P32320''P32321''P32455''P32456''P32926''P32927''P32942''P32970''P32971''P33121''P33151''P33241''P33316''P33681''P33764''P34096''P34130''P34896''P34910''P34913''P34947''P34949''P34998''P35052''P35070''P35218''P35219''P35221''P35225''P35228''P35237''P35247''P35249''P35318''P35442''P35443''P35475''P35520''P35542''P35556''P35579''P35590''P35606''P35609''P35611''P35613''P35625''P35637''P35754''P35813''P35914''P35916''P35968''P36222''P36269''P36551''P36776''P36873''P36888''P36897''P36941''P36952''P36955''P36959''P36980''P37023''P37058''P37108''P37173''P37235''P37837''P37840''P38484''P38935''P38936''P39059''P39060''P39748''P39900''P39905''P40121''P40189''P40197''P40198''P40199''P40222''P40225''P40259''P40313''P40818''P40925''P40933''P41159''P41208''P41217''P41218''P41222''P41227''P41236''P41271''P41439''P41586''P41732''P42081''P42331''P42574''P42575''P42658''P42681''P42701''P42702''P42768''P42785''P42830''P42892''P43007''P43121''P43146''P43166''P43220''P43234''P43251''P43320''P43357''P43378''P43487''P43489''P43490''P43627''P43628''P43629''P43630''P43632''P43652''P45452''P45954''P45984''P46013''P46060''P46109''P46379''P46531''P46783''P46926''P46937''P47712''P47813''P47874''P47928''P47929''P47972''P47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panel'Cardiometabolic''Cardiometabolic_II''Inflammation''Inflammation_II''Neurology''Neurology_II''Oncology''Oncology_II'
Schema
Section titled “Schema”| Column | Type | Description |
|---|---|---|
ancestry |
TEXT |
Partition column. Population ancestry code: ALL = all ancestries combined, AFR = African, AMR = Admixed American, CSA = Central-South Asian, EAS = East Asian, EUR = European, MID = Middle Eastern. |
protein_id |
TEXT |
Partition column. UniProt accession. Get this from assays table if you have a gene symbol. |
panel |
TEXT |
Partition column. Olink panel containing the assay. |
chromosome |
TEXT |
Chromosome on which the variant is located. |
position_grch37 |
INT |
Variant position in assembly GRCh37 coordinates. |
position_grch38 |
INT |
Variant position in assembly GRCh38 coordinates. |
effect_allele |
TEXT |
Effect allele. Harmonized to equal the dbSNP alt_allele. |
other_allele |
TEXT |
Non-effect allele. Harmonized to equal the dbSNP ref_allele. |
beta |
FLOAT |
Effect size estimate, oriented to effect_allele after harmonization (sign flipped where the source allele assignment was swapped). |
standard_error |
FLOAT |
Standard error of the effect size estimate. |
effect_allele_frequency |
FLOAT |
Frequency of the effect allele in the ancestry group, oriented to effect_allele after harmonization (set to 1 - source frequency where the source allele assignment was swapped). |
neg_log_10_p_value |
FLOAT |
-log10(p-value). Higher = more significant. Genome-wide significance threshold is ~7.3. |
variant_id |
TEXT |
Unique UKB-PPP variant identifier (e.g. 4:180574458:A:G:imp:v1). |
info |
FLOAT |
Imputation quality score (0-1, higher is better). |
n |
INT |
Sample size. |
chi_squared |
FLOAT |
Chi-squared test statistic. |
in_dbsnp |
BOOLEAN |
True if the variant was matched to dbSNP during harmonization. Filter to in_dbsnp = True to exclude variants whose alleles could not be validated against a reference (effect_allele/other_allele orientation and beta sign should be considered unreliable when False). |
is_palindromic |
BOOLEAN |
Variant alleles are A/T or C/G. These require specific treatment during harmonization and are typically excluded from cross-cohort analyses. |