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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...plot of the regions flanking the histone locus. Values between double-headed arrows under the x-axis indicate the r2 measure of linkage disequilibrium between the variants spanned by the arrows. Coordinates are with respect to the histone locus, with negative values indicating the distal flank...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...enhancers in the brain, which identified ∼79,000 brain-specific enhancers (Wang et al. 2018). We identified a high-confidence set of PFC enhancers (18,212 regions) based on strong ATAC-seq and DNase signals, as well as strong H3K27ac signals from both the Roadmap PFC and PsychENCODE PFC ChIP-seq experiments...
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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...conservation alone as we see no significant difference in GERP scores between nominally P < 0.001 significant and nonsignificant ASB variants in neuron-specific peaks (t-test, P-value = 0.32) or between cell types (P-value = 0.61).ASB in -wide association studiesWe performed stratified linkage disequilibrium...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole- resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits Olivia Corradin 1 , Alina Saiakhova 1 , Batool Akhtar-Zaidi 1 , Lois Myeroff 2 , Joseph...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome Jessica Stapley 1 , Tim R. Birkhead , Terry Burke and Jon Slate Department of Animal and Plant Sciences, University of Sheffield...
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ARTICLE: Extensive and breed-specific linkage disequilibrium in Canis familiaris
- Nathan B. Sutter,
- Michael A. Eberle,
- Heidi G. Parker,
- Barbara J. Pullar,
- Ewen F. Kirkness,
- Leonid Kruglyak,
- and Elaine A. Ostrander
Genome Res. December 2004 14: 2388-2396; Published in Advance November 15, 2004, doi:10.1101/gr.3147604
....A., Bhattacharyya, S., Leaves, N.I., Anderson, G.G., Zhang, Y., Lench, N.J., Carey, A., et al. 2001 . Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68 : 191 -197. ↵ Akey, J.M., Zhang, G., Zhang, K., Jin, L., and Shriver, M.D. 2002 . Interrogating a high-density SNP...
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ARTICLE: Extensive Genome-wide Linkage Disequilibrium in Cattle
- Frédéric Farnir,
- Wouter Coppieters,
- Juan-José Arranz,
- Paulette Berzi,
- Nadine Cambisano,
- Bernard Grisart,
- Latifa Karim,
- Fabienne Marcq,
- Laurence Moreau,
- Myriam Mni,
- Carine Nezer,
- Patricia Simon,
- Pascal Vanmanshoven,
- Danny Wagenaar,
- and Michel Georges
Genome Res. February 1, 2000 10: 220-227; doi:10.1101/gr.10.2.220
..., Toronto ). ↵ Spielman R.S. , Ginnis R.E. , Ewens W.J. ( 1993 ) Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52 : 506 – 516 . ↵ Stephens J.C. , Briscoe D. , O'Brien S.J. ( 1994 ) Mapping by admixture linkage...
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LETTER: Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes
- Penelope E. Bonnen,
- Peggy J. Wang,
- Marek Kimmel,
- Ranajit Chakraborty,
- and David L. Nelson
Genome Res. December 1, 2002 12: 1846-1853; Published in Advance November 12, 2002, doi:10.1101/gr.483802
...of chromosomes accounted for by the shared haplotypes with 59% and 49%, respectively. Although the amount of sharing varies by ethnic group and locus, it is substantial in all. LD Analyses The pattern and extent of linkage disequilibrium (LD) at each genomic region differed widely. LD was measured using...

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