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Global patterns of cis variation in human cells revealed by high-density allelic expression analysis
- Source :
- Nature Genetics. 41:1216-1222
- Publication Year :
- 2009
- Publisher :
- Springer Science and Business Media LLC, 2009.
-
Abstract
- Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.
- Subjects :
- musculoskeletal diseases
Genetics
Transcription, Genetic
Gene Expression Profiling
genetic processes
Genetic Variation
High density
pathological conditions, signs and symptoms
Biology
Polymorphism, Single Nucleotide
Cell Line
persons
Variation (linguistics)
Lymphoblastoid cell
Expression analysis
Humans
Lupus Erythematosus, Systemic
natural sciences
Lymphocytes
Allele
International HapMap Project
Alleles
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 15461718 and 10614036
- Volume :
- 41
- Database :
- OpenAIRE
- Journal :
- Nature Genetics
- Accession number :
- edsair.doi.dedup.....c24532e4d8f574e96c6827d9fb854d34