Table 4.

Methods and conclusions from screens for allele-specific chromatin and ASTF at non-imprinted loci

Tissues or cell types (n)	Primary screening methods and validations	Findings and conclusions	References
LCL (12; from 2 CEPH families)	RNA PolII and histone modification ChIP–Chip on Affy 10K SNP arrays; ChIP antibodies validated by Q-PCR of IPs at imprinted loci	ASTF as measured by PolII occupancy and chromatin modifications (H3K4, H3K9, H3K27 methylation state) behaves as a genetically determined trait in families	(60)
IMR90 fibroblast line (1)	RNA PolII ChIP-SNP on Illumina Hap300 BeadChips; validations by PCR sequencing of IPs; ASE by cDNA/gDNA comparison using Illumina GoldenGate assays	Of 11 9821 heterozygous SNPS, 466 (239 RefSeq genes and 18 small RNAs) showed allele-specific enrichment in PolII IPs with an average fold change of 3.98. For 20 examples among these genes, the allele-specific RNA PolII binding was shown to correlate with ASE in the IMR90 cells.	(61); see also (62)
LCL (10)	RNA PolII and NF-κB ChIP-Seq data overlaid to SNP genotypes from HapMap and CNVs	SNPs and structural variants are frequently associated with RNA PolII and NF-κB binding differences. The fraction of binding differences coinciding with genetic variations can be very high: 35% for NF-κB and 26% for PolII in these LCLs	(63)
LCL (6; 4 parents and 2 children from HapMap project)	DNase I HS site (DNase-Seq) mapping and ChIP-Seq for CTCF–binding sites; validations by PCR/MS (Sequenom) on ChIP material	Transmission of SNP alleles suggests a heritable genetic basis for a large proportion of the allele-specific binding of CTCF. At sites where CTCF showed ASTF, the binding motif score tended to be higher for the favored allele, whereas at sites lacking differences in CTCF binding, motif scores were similar	(41)

All experiments include internal statistical validations of the microarray data; secondary validations refer to downstream assays by independent methods. Cells and tissues are of human origin.