FABIAN-variant
RESTful API Standalone version
GeneCascade
Berlin Institute of Health
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Example: ACKR1 promoter mutation

This mutation in the promoter of ACKR1 (OMIM: 613665) disrupts GATA1 binding. Either leave the transcription factor selection unchanged ('Known TFBSs ...') or choose 'Select individually...' and select GATA1. Then click 'Analyse'.

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Example: Shh limb enhancer variant (mouse)

This variant in the ZRS, the limb enhancer of the mouse Shh gene (rs212269559), creates an AP-1 (Fos/Jun) binding site. Heterodimers have been set to 'shown separately', so Fos::Jun and Batf::Jun also appear. Click 'Analyse' to see the results.

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Example: Sample VCF file

The VCF file TinyExample38.vcf contains three variants to illustrate the file format:

2	127418425	.	T	C	116	PASS	.	GT:DP	0/1:154
10	6051177	.	G	A	116	PASS	.	GT:DP	0/1:154
X	80014682	.	G	A	116	PASS	.	GT:DP	0/1:154
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Example: Sample mouse VCF file

The VCF file TinyExampleMm39.vcf contains three variants (GRCm39) in the ZRS, the limb-specific enhancer of the mouse Shh gene:

chr5	29519996	.	C	T	100	PASS	.	GT:DP	0/1:30
chr5	29520085	.	G	A	100	PASS	.	GT:DP	0/1:30
chr5	29520096	.	A	T	100	PASS	.	GT:DP	0/1:30
Enter sequences directly Show an example
Format info
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Accepted formats:

1:159204893T>C
1:159.204.893T>C
chr1:g.159,204,893T>C
1-159204893-T-C
1 159204893 . T C
1 159204893 T C Default
Thousands separator
HGVS-like
gnomAD
VCF
VCF without ID

For indels, use the VCF format: always start with the last reference base before the variant.

The genome build must match the chromosomal annotation (GRCh37/hg19 or GRCh38/hg38 for human, GRCm38/mm10 or GRCm39/mm39 for mouse).

Format info
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The reference and variant sequences may contain only the letters A, C, G, and T. Sequences of about 30 bases are recommended.

Known transcription factor binding sites cannot be searched in this interface, as no genomic location is provided.

Search starts after two characters are entered.

Selected:

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

1:159204893T>C
1:159.204.893T>C
chr1:g.159,204,893T>C
1-159204893-T-C
1 159204893 . T C
1 159204893 T C Default
Thousands separator
HGVS-like
gnomAD
VCF
VCF without ID

For indels, use the VCF format: always start with the last reference base before the variant.

The genome build must match the chromosomal annotation (GRCh37/hg19 or GRCh38/hg38 for human, GRCm38/mm10 or GRCm39/mm39 for mouse).

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

Format info
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Accepted format:

<Ref> <Alt>
<Ref> <Alt>
<Ref> <Alt>
...

where each <Ref> sequence and <Alt> sequence may contain only the letters A, C, G, and T. A space separates <Ref> and <Alt>, and a newline separates two variants.

<Ref> and <Alt> sequences of about 30 bases are recommended.

Up to 100 variants can be submitted in this interface.

Known transcription factor binding sites cannot be searched in this interface, as no genomic location is provided.

Show an example
Format info
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Input files must be in VCF format. Support for multi-sample VCF files is limited. Only the first sample is considered.

Click 'Show an example' to load a sample VCF file. The tutorial contains a public whole-genome sequencing VCF file.

The documentation also describes how the VCF fields are processed.

Use the options below to restrict the analysis to variants near selected genes or regions.

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

Please zip or gzip large VCF files before upload.