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Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Abstract：

:Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome.

journal_name

Hum Genet

journal_title

Human genetics

authors

Cavalli M,Pan G,Nord H,Wallerman O,Wallén Arzt E,Berggren O,Elvers I,Eloranta ML,Rönnblom L,Lindblad Toh K,Wadelius C

doi

10.1007/s00439-016-1654-x

subject

Has Abstract

pub_date

2016-05-01 00:00:00

pages

485-497

issue

5

eissn

0340-6717

issn

1432-1203

pii

10.1007/s00439-016-1654-x

journal_volume

135

pub_type

杂志文章

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