Other apps
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Example: Disease mutation CHRND_L63P

This is an example of a mutation in the promoter of PIGM which disrupts SP1 binding.

You can either leave the choice of transcription factors as it is ('Known TFBSs') or manually choose SP1.

After you are finished, click on 'Analyse'.

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Example: Tiny sample VCF file

The VCF file TinyExample.vcf only contains three lines to illustrate the file format:

3	190122694	.	G	A	116	.	.	GT:DP	0/1:154
1	984171	.	CAG	C	116	.	.	GT:DP	0/1:154
21	33036170	.	A	G	116	.	.	GT:DP	0/1:154
Enter sequences directly Show an example
Format info
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Accepted formats:

17:38244559C>T
17:38.244.559C>T
chr17:g.38,244,559C>T
17-38244559-C-T
17 38244559 . C T
17 38244559 C T Default
Thousands separator
HGNC SNV
gnomAD
VCF
VCF without ID

For InDels, use the VCF format, i.e. always start with the last reference base before the variant.

GRCh37/hg19 or GRCh38/hg38 must match the chromosomal annotation.

Format info
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The wild-type sequence and variant sequence may consist of letters ACGT. We suggest to use sequences of about 30 bases.

Please note that searching for known transcription factor binding sites is not possible in this interface (missing the genomic location).

Search starts after two characters are entered.

Selected:

Enter sequences directly Show an example
Format info
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Accepted formats per line:

17:38244559C>T
17:38.244.559C>T
chr17:g.38,244,559C>T
17-38244559-C-T
17 38244559 . C T
17 38244559 C T Default
Thousands separator
HGNC SNV
gnomAD
VCF
VCF without ID

For InDels, use the VCF format, i.e. always start with the last reference base before the variant.

GRCh37/hg19 or GRCh38/hg38 must match the chromosomal annotation.

Up to 100 variants can be submitted in this interface. Please use the VCF file interface if you need to analyze more variants.

Format info
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Accepted format:

<WT> <MT>
<WT> <MT>
<WT> <MT>
...

where each <WT> sequence and <MT> sequence may consist of letters ACGT. A space character is used to separate <WT> and <MT> and a newline character to separate two variants.

We suggest to use <WT> and <MT> sequences of about 30 bases.

Up to 100 variants can be submitted in this interface.

Please note that searching for known transcription factor binding sites is not possible in this interface (missing the genomic location).

Show options Show an example
Format info
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Input files have to be in VCF format. Up to now, we do not offer processing of (merged) VCF files containing variants obtained from sequencing of two or more samples. Thus, the uploaded VCF file may only contain data from one sample.

An Example of a VCF file can be selected by clicking on 'Show an example'. The tutorial contains a public whole genome sequencing VCF file.

Details on the processing of the VCF fields can also be found in the documentation.

Click on 'Show options' to restrict variants around candidate genes or regions.

By default, FABIAN-variant will analyze up to 10,000 variants in the VCF file.

Please zip or gzip large VCF files before upload.

The following options are selected:
Coverage < 10, homozygous in ≥ 10 gnomAD or ExAC samples or ≥ 4 1000G samples