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Figure 4 | Genome Medicine

Figure 4

From: Identification of cis-regulatory sequence variations in individual genome sequences

Figure 4

Visualization of a causal cis- regulatory mutation for hemophilia B Leyden that alters an HNF4A binding site in the promoter of the Factor IX gene. In this example, at least three sets of data support the hypothesis that the variant modifies a functional transcription factor binding site (TFBS): a TFBS database, proximity to a transcription start site (TSS; topology filter), and conservation data. (a) Variant location in base pairs between the regulatory element and the TSS. (b) Logo of nucleotide binding preferences for HNF4a. The mutated position in the HNF4A binding site is highlighted. The height of the letters 'T' and 'A' at that position indicate the frequency of a thymine or an adenine nucleotide in HNF4a TFBSs. The thymine at position 8 is strongly maintained among known TFBSs. (c) UCSC Genome Browser view highlighting four of the data types that may be used to support the prediction of a cis-regulatory variant. Red and gold tracks, PAZAR and ORegAnno databases of TFBSs; dark blue track, mammalian conservation; black track, data from dbSNP.

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