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. 2020 Feb 7;11:778. doi: 10.1038/s41467-020-14499-3

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Illustrates the association of the observed common nine haplotypes formed by the seven AMD-associated CFH locus variants considered in our association analyses and rs6677604 (overall haplotype frequency ≥1% in the Cambridge and EUGENDA cohorts combined, accounting for 98.5% of 2012 chromosomes) with AMD and with FHR-4/FH levels. Details of the alleles forming the haplotypes together with the frequency distribution in the two cohorts combined, and as estimated in the IAMDGC dataset⁵ (16,144 patients with advanced AMD and 17,832 controls of European ancestry), are shown in b: haplotype CTTGCCGC (H1) that carries the AMD increasing-risk allele T of the proxy for Y402H (1.2) is used as reference (coloured in red); alleles that are different from the reference are coloured in blue; the direction of association with AMD for the minor allele of each single variant as estimated in the IAMDGC study⁵ is indicated within parentheses. Four association plots are displayed in a: the first two (top) plots show the OR (with CI) estimates for the CFH haplotype association with AMD in the IAMDGC dataset and our two-cohort meta-analysis, respectively; the third and fourth (bottom) plots show the β (with CI) estimates for the CFH haplotype association with FHR-4 and FH levels, respectively, in our two-cohort meta-analysis; haplotype H1 is used as reference. The estimates shown in each plot are labelled further to indicate the presence of alleles that differ from the reference; those alleles are indicated with the IAMDGC association signal numbers of the corresponding variants (1.1, 1.5–1.7), in red to indicate that the allele different from the reference is AMD risk-increasing allele, in blue if protective; the Y402H label is blue to indicate the presence of the protective allele G of variant 1.2, red for the AMD risk-increasing allele T; finally, the label DEL indicates the presence of the protective allele A of the proxy for the CFHR1-3 deletion (rs6677604). See Supplementary Data 9 for full details of the haplotype association estimates. Source data are provided as a Source Data file.