UCSC browser views of our data

The links below load selected regions (including the figures from the paper) in the UCSC genome browser. They initially show seleted regions but allow you to navigate the entire genome. All of the analyses are based on the March 2006 (hg18) genome assembly.

There is a link to download the data file, some other views of the data and useful links further down.

chr15:22,651,568-22,832,882 SNP_A-1932077 SNRPN
chr2:80,102,199-80,426,846 SNP_A-8486811 LRRTM1
chr2:130,390,000-130,510,000 SNP_A-1921713 RAB6C
chr11:132,322,501-132,472,5000 SNP_A-2002432 OPCML
chr5:160,187,340-160,309,082 SNP_A-1782879 ATP10B
chr11:2,850,000-3,000,000 SNP_A-4258853 NAP1L4
chr13:23,856,317-24,131,956 SNP_A-2065646 PARP4
chr19:46,310,524-46,354,407 SNP_A-8631787 CYP2F1
chr3:46,449,610-46,492,959 SNP_A-1972595 LTF
chr21:45,677,275-45,802,028 SNP_A-2020619 COL18A1
chr15:57,678,933-57,706,359 SNP_A-1859378 GCNT3
chr6:37,065,060-37,270,509 SNP_A-4250374 FGD2
chr14:99,260,000-99,320,000 SNP_A-8638885 CYP46A1
chr1:22,100,000-22,300,000 SNP_A-1795087 CELA3b
five-track data file ...

Amplicon tracks

Display of amplicon fragments. Pale grey indicates no sites for the methylation-sensitive enzymes used in our assay
amplicon track data file ... amplicon track-ucsc browser

Amplicon fragments as above, but showing only those where in our sample there are heterozygous (informative) SNPs.
filtered amplicon track data file ... amplicon track-ucsc browser

Average of the 5 twin pairs

average data file ... RAS average-ucsc browser

List of 2,704 SNPs with an average RAS change above 0.10 in heterozygous individuals

Table of probesets with RAS difference > 0.1 with names of associated genes

Allelic expression data adapted from Ge et al

Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KC, Gagné, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Göring HH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T. (2009) Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet. 41(11):1216-22.

average AE data file ... AE average-ucsc browser

Overlap between ASM and AE

Overlap between genes near a SNP with a RAS change >0.1 and those containing a SNP found to have an ASE score >0.1 by Ge et al (2009)

Individual twin pairs

family 2411-data file ... family 2411-ucsc browser

family 1990-data file ... family 1990-ucsc browser

family 3268-data file ... family 3268-ucsc browser

family 2436-data file ... family 2436-ucsc browser

family 5128-data file ... family 5128-ucsc browser

Gene expression data

gene expression data Gene expression data for detectable transcripts located within 5kb of SNPs with a RAS change ≥ 0.10 after MSRE digestion

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

Ryan McDaniell, Bum-Kyu Lee, Lingyun Song, Zheng Liu, Alan P. Boyle, Michael R. Erdos, Laura J. Scott, Mario A. Morken, Katerina S. Kucera, Anna Battenhouse, Damian Keefe, Francis S. Collins, Huntington F. Willard, Jason D. Lieb, Terrence S. Furey, Gregory E. Crawford, Vishwanath R. Iyer, and Ewan Birney (2010) Signatures in Humans Science [DOI: 10.1126/science.1184655]

view of ASM, AE and McDaniell data currently this shows the 'open chromatin' measures and not the allele-specific aspect.