This site is a freely accessible, searchable database of affinity altering SNPs (aaSNPs) for the nuclear receptor superfamily of ligand-dependent transcription factors (TFs) and other TFs of interest. aaSNPs in the regulatory region of human genes are determined by Protein Binding Microarrays (PBMs) and cross referenced with publicly available ChIP-seq data.

Affinity altering SNP (aaSNP): a single nucleotide polymorphism that significantly changes the binding affinity of a transcription factor for a given DNA sequence.

Protein Binding Microarray (PBM): a high throughput DNA binding assay in which a TF is applied to a glass slide with 1000's of spots of DNA, each with a unique sequence.

Please note that as comprehensive as these data may appear, not all SNPs (>30M) can be reasonably assayed in the PBM.

Field definitions

PBM

Protein binding microarray designs

SNP-PBM

Genetic variants extracted from promotors (-6 kb to +1 kb) relative to transcription start sites (TSS) of 3,000 disease and phenotype associated genes

HNF4a ChIP-SNP-PBM

Genetic variants extracted from 200 bp window around peak center of HNF4a & RXRa ChIP-seq peaks from HepG2 and CaCo-2 cell lines [1,2]

GTEx Liver

eQTLs mined from the GTEx Project associated with Liver gene expression changes

Chr

Chromosome of genetic variant

Pos

Position on chromosome of genetic variant

Variant

Genetic variant identifier. Formatted as chr_pos_ref_alt_build. This is the GTEx Project identifier for GTEx related designs

Nearest Gene

Official gene symbol of the nearest TSS

Ref Score

PBM binding score of the Reference allele (first in ID)

Alt Score

PBM binding score of the Alternate allele (second in ID)

Test Seq

Test sequence (variant + 14 nt flanking) of the Reference allele

Cohen's

Cohen's D effect size estimator for the difference in binding affinity between Ref & Alt alleles

Obs. Diff.

The observed difference (Alt-Ref) between alleles

padj.

Benjamini-Hochberg corrected P-values for the difference in binding affinity between Ref & Alt alleles

Slope

Slope (Beta) of the eQTL associated change in gene expression. When scores are positive (+) associated gene is expressed more highly in individuals homozygous for Alternate alleles

P-value

Gene symbol of the gene associated with a change of gene expression (eGene) from eQTL identified in GTEx Project

Gene

Gene symbol of the gene associated with a change of gene expression (eGene) from eQTL identified in GTEx Project

Please see Nuclear Receptor DNA Binding Project (http://nrdbs.ucr.edu/) for additional information and references.