{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T13:46:24Z","timestamp":1776001584033,"version":"3.50.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,5,31]],"date-time":"2023-05-31T00:00:00Z","timestamp":1685491200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Portuguese funds","award":["PTDC\/MEC-NEU\/29486\/2017"],"award-info":[{"award-number":["PTDC\/MEC-NEU\/29486\/2017"]}]},{"name":"Programa de Coopera\u00e7\u00e3o Transfronteiri\u00e7a Interreg VA Espa\u00f1a-Portugal"},{"DOI":"10.13039\/501100008530","name":"Fundo Europeu de Desenvolvimento Regional","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Most SNPs associated with complex diseases seem to lie in non-coding regions of the genome; however, their contribution to gene expression and disease phenotype remains poorly understood. Here, we established a workflow to provide assistance in prioritising the functional relevance of non-coding SNPs of candidate genes as susceptibility loci in polygenic neurological disorders. To illustrate the applicability of our workflow, we considered the multifactorial disorder migraine as a model to follow our step-by-step approach. We annotated the overlap of selected SNPs with regulatory elements and assessed their potential impact on gene expression based on publicly available prediction algorithms and functional genomics information.<\/jats:p>\n               <jats:p>Some migraine risk loci have been hypothesised to reside in non-coding regions and to be implicated in the neurotransmission pathway. In this study, we used a set of 22 non-coding SNPs from neurotransmission and synaptic machinery-related genes previously suggested to be involved in migraine susceptibility based on our candidate gene association studies. After prioritising these SNPs, we focused on non-reported ones that demonstrated high regulatory potential: (1) VAMP2_rs1150 (3\u2032 UTR) was predicted as a target of hsa-mir-5010-3p miRNA, possibly disrupting its own gene expression; (2) STX1A_rs6951030 (proximal enhancer) may affect the binding affinity of zinc-finger transcription factors (namely ZNF423) and disturb TBL2 gene expression; and (3) SNAP25_rs2327264 (distal enhancer) expected to be in a binding site of ONECUT2 transcription factor.<\/jats:p>\n               <jats:p>This study demonstrated the applicability of our practical workflow to facilitate the prioritisation of potentially relevant non-coding SNPs and predict their functional impact in multifactorial neurological diseases.<\/jats:p>","DOI":"10.1093\/bfgp\/elad020","type":"journal-article","created":{"date-parts":[[2023,5,31]],"date-time":"2023-05-31T06:12:58Z","timestamp":1685513578000},"page":"138-149","source":"Crossref","is-referenced-by-count":5,"title":["Integrating functional scoring and regulatory data to predict the effect of non-coding SNPs in a complex neurological disease"],"prefix":"10.1093","volume":"23","author":[{"given":"Daniela","family":"Fel\u00edcio","sequence":"first","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) , Porto 4200-135 , Portugal"},{"name":"Instituto Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS), Universidade do Porto , Porto 4050-313 , Portugal"}]},{"given":"Miguel","family":"Alves-Ferreira","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Instituto Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS), Universidade do Porto , Porto 4050-313 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), , Porto 4200-135 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Centre for Predictive and Preventive Genetics (CGPP), , Porto 4200-135 , Portugal"}]},{"given":"Mariana","family":"Santos","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), , Porto 4200-135 , Portugal"}]},{"given":"Marlene","family":"Quintas","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Instituto Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS), Universidade do Porto , Porto 4050-313 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), , Porto 4200-135 , Portugal"}]},{"given":"Alexandra M","family":"Lopes","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) , Porto 4200-135 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Centre for Predictive and Preventive Genetics (CGPP), , Porto 4200-135 , Portugal"}]},{"given":"Carolina","family":"Lemos","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Instituto Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS), Universidade do Porto , Porto 4050-313 , Portugal"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), , Porto 4200-135 , Portugal"}]},{"given":"N\u00e1dia","family":"Pinto","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) , Porto 4200-135 , Portugal"},{"name":"Centro de Matem\u00e1tica da Universidade do Porto (CMUP) , Porto 4169-007 , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3720-2920","authenticated-orcid":false,"given":"Sandra","family":"Martins","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (i3S) , Porto 4200-135 , Portugal"},{"name":"Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) , Porto 4200-135 , Portugal"}]}],"member":"286","published-online":{"date-parts":[[2023,5,30]]},"reference":[{"key":"2024053000062266900_ref1","doi-asserted-by":"crossref","first-page":"R102","DOI":"10.1093\/hmg\/ddv259","article-title":"Non-coding genetic variants in human disease","volume":"24","author":"Zhang","year":"2015","journal-title":"Hum Mol Genet"},{"key":"2024053000062266900_ref2","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/bib\/bby039","article-title":"Regulatory variants: from detection to predicting impact","volume":"20","author":"Rojano","year":"2019","journal-title":"Brief 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