region to annotate genome position or search term

Your session doesn't have any custom tracks or hub tracks in pgSnp or VCF format.   
variants: Artificial Example Variants HGVS terms Variant Identifiers
maximum number of variants to be processed: 10 100 1,000 10,000 100,000
The gene predictions selected here will be used to determine the effect of each variant on genes, for example intronic, missense, splice site, intergenic etc.
NCBI RefSeq Historical Transcript Versions NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD NCBI RefSeq Select and MANE subset: A single representative transcript UCSC annotations of RefSeq RNAs (NM_* and NR_*) NCBI RefSeq genes, predicted subset (XM_* or XR_*) NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) GENCODE V43 GENCODE V39 GENCODE V38 GENCODE V36 PolyA Transcript Annotation Set from GENCODE Version 50 (Ensembl 116) Pseudogene Annotation Set from GENCODE Version 50 (Ensembl 116) Comprehensive Gene Annotation Set from GENCODE Version 50 (Ensembl 116) Basic Gene Annotation Set from GENCODE Version 50 (Ensembl 116) PolyA Transcript Annotation Set from GENCODE Version 49 (Ensembl 115) Pseudogene Annotation Set from GENCODE Version 49 (Ensembl 115) Comprehensive Gene Annotation Set from GENCODE Version 49 (Ensembl 115) Basic Gene Annotation Set from GENCODE Version 49 (Ensembl 115) PolyA Transcript Annotation Set from GENCODE Version 48 (Ensembl 114) Pseudogene Annotation Set from GENCODE Version 48 (Ensembl 114) Comprehensive Gene Annotation Set from GENCODE Version 48 (Ensembl 114) Basic Gene Annotation Set from GENCODE Version 48 (Ensembl 114) PolyA Transcript Annotation Set from GENCODE Version 47 (Ensembl 113) Pseudogene Annotation Set from GENCODE Version 47 (Ensembl 113) Comprehensive Gene Annotation Set from GENCODE Version 47 (Ensembl 113) Basic Gene Annotation Set from GENCODE Version 47 (Ensembl 113) PolyA Transcript Annotation Set from GENCODE Version 46 (Ensembl 112) Pseudogene Annotation Set from GENCODE Version 46 (Ensembl 112) Comprehensive Gene Annotation Set from GENCODE Version 46 (Ensembl 112) Basic Gene Annotation Set from GENCODE Version 46 (Ensembl 112) PolyA Transcript Annotation Set from GENCODE Version 45 (Ensembl 111) Pseudogene Annotation Set from GENCODE Version 45 (Ensembl 111) Comprehensive Gene Annotation Set from GENCODE Version 45 (Ensembl 111) Basic Gene Annotation Set from GENCODE Version 45 (Ensembl 111) PolyA Transcript Annotation Set from GENCODE Version 44 (Ensembl 110) Pseudogene Annotation Set from GENCODE Version 44 (Ensembl 110) Comprehensive Gene Annotation Set from GENCODE Version 44 (Ensembl 110) Basic Gene Annotation Set from GENCODE Version 44 (Ensembl 110) PolyA Transcript Annotation Set from GENCODE Version 43 (Ensembl 109) Pseudogene Annotation Set from GENCODE Version 43 (Ensembl 109) Comprehensive Gene Annotation Set from GENCODE Version 43 (Ensembl 109) Basic Gene Annotation Set from GENCODE Version 43 (Ensembl 109) PolyA Transcript Annotation Set from GENCODE Version 42 (Ensembl 108) Pseudogene Annotation Set from GENCODE Version 42 (Ensembl 108) Comprehensive Gene Annotation Set from GENCODE Version 42 (Ensembl 108) Basic Gene Annotation Set from GENCODE Version 42 (Ensembl 108) PolyA Transcript Annotation Set from GENCODE Version 41 (Ensembl 107) Pseudogene Annotation Set from GENCODE Version 41 (Ensembl 107) Comprehensive Gene Annotation Set from GENCODE Version 41 (Ensembl 107) Basic Gene Annotation Set from GENCODE Version 41 (Ensembl 107) 2-way Pseudogene Annotation Set from GENCODE Version 41 (Ensembl 107) PolyA Transcript Annotation Set from GENCODE Version 40 (Ensembl 106) Pseudogene Annotation Set from GENCODE Version 40 (Ensembl 106) Comprehensive Gene Annotation Set from GENCODE Version 40 (Ensembl 106) Basic Gene Annotation Set from GENCODE Version 40 (Ensembl 106) 2-way Pseudogene Annotation Set from GENCODE Version 40 (Ensembl 106) PolyA Transcript Annotation Set from GENCODE Version 39 (Ensembl 105) Pseudogene Annotation Set from GENCODE Version 39 (Ensembl 105) Comprehensive Gene Annotation Set from GENCODE Version 39 (Ensembl 105) Basic Gene Annotation Set from GENCODE Version 39 (Ensembl 105) 2-way Pseudogene Annotation Set from GENCODE Version 39 (Ensembl 105) PolyA Transcript Annotation Set from GENCODE Version 38 (Ensembl 104) Pseudogene Annotation Set from GENCODE Version 38 (Ensembl 104) Comprehensive Gene Annotation Set from GENCODE Version 38 (Ensembl 104) Basic Gene Annotation Set from GENCODE Version 38 (Ensembl 104) 2-way Pseudogene Annotation Set from GENCODE Version 38 (Ensembl 104) PolyA Transcript Annotation Set from GENCODE Version 37 (Ensembl 103) Pseudogene Annotation Set from GENCODE Version 37 (Ensembl 103) Comprehensive Gene Annotation Set from GENCODE Version 37 (Ensembl 103) Basic Gene Annotation Set from GENCODE Version 37 (Ensembl 103) 2-way Pseudogene Annotation Set from GENCODE Version 37 (Ensembl 103) PolyA Transcript Annotation Set from GENCODE Version 36 (Ensembl 102) Pseudogene Annotation Set from GENCODE Version 36 (Ensembl 102) Comprehensive Gene Annotation Set from GENCODE Version 36 (Ensembl 102) Basic Gene Annotation Set from GENCODE Version 36 (Ensembl 102) 2-way Pseudogene Annotation Set from GENCODE Version 36 (Ensembl 102) PolyA Transcript Annotation Set from GENCODE Version 35 (Ensembl 101) Pseudogene Annotation Set from GENCODE Version 35 (Ensembl 101) Comprehensive Gene Annotation Set from GENCODE Version 35 (Ensembl 101) Basic Gene Annotation Set from GENCODE Version 35 (Ensembl 101) 2-way Pseudogene Annotation Set from GENCODE Version 35 (Ensembl 101) PolyA Transcript Annotation Set from GENCODE Version 34 (Ensembl 100) Pseudogene Annotation Set from GENCODE Version 34 (Ensembl 100) Comprehensive Gene Annotation Set from GENCODE Version 34 (Ensembl 100) Basic Gene Annotation Set from GENCODE Version 34 (Ensembl 100) 2-way Pseudogene Annotation Set from GENCODE Version 34 (Ensembl 100) PolyA Transcript Annotation Set from GENCODE Version 33 (Ensembl 99) Pseudogene Annotation Set from GENCODE Version 33 (Ensembl 99) Comprehensive Gene Annotation Set from GENCODE Version 33 (Ensembl 99) Basic Gene Annotation Set from GENCODE Version 33 (Ensembl 99) 2-way Pseudogene Annotation Set from GENCODE Version 33 (Ensembl 99) PolyA Transcript Annotation Set from GENCODE Version 32 (Ensembl 98) Pseudogene Annotation Set from GENCODE Version 32 (Ensembl 98) Comprehensive Gene Annotation Set from GENCODE Version 32 (Ensembl 98) Basic Gene Annotation Set from GENCODE Version 32 (Ensembl 98) 2-way Pseudogene Annotation Set from GENCODE Version 32 (Ensembl 98) PolyA Transcript Annotation Set from GENCODE Version 31 (Ensembl 97) Pseudogene Annotation Set from GENCODE Version 31 (Ensembl 97) Comprehensive Gene Annotation Set from GENCODE Version 31 (Ensembl 97) Basic Gene Annotation Set from GENCODE Version 31 (Ensembl 97) 2-way Pseudogene Annotation Set from GENCODE Version 31 (Ensembl 97) PolyA Transcript Annotation Set from GENCODE Version 30 (Ensembl 96) Pseudogene Annotation Set from GENCODE Version 30 (Ensembl 96) Comprehensive Gene Annotation Set from GENCODE Version 30 (Ensembl 96) Basic Gene Annotation Set from GENCODE Version 30 (Ensembl 96) 2-way Pseudogene Annotation Set from GENCODE Version 30 (Ensembl 96) PolyA Transcript Annotation Set from GENCODE Version 29 (Ensembl 94) Pseudogene Annotation Set from GENCODE Version 29 (Ensembl 94) Comprehensive Gene Annotation Set from GENCODE Version 29 (Ensembl 94) Basic Gene Annotation Set from GENCODE Version 29 (Ensembl 94) 2-way Pseudogene Annotation Set from GENCODE Version 29 (Ensembl 94) PolyA Transcript Annotation Set from GENCODE Version 28 (Ensembl 92) Pseudogene Annotation Set from GENCODE Version 28 (Ensembl 92) Comprehensive Gene Annotation Set from GENCODE Version 28 (Ensembl 92) Basic Gene Annotation Set from GENCODE Version 28 (Ensembl 92) 2-way Pseudogene Annotation Set from GENCODE Version 28 (Ensembl 92) PolyA Transcript Annotation Set from GENCODE Version 27 (Ensembl 90) Pseudogene Annotation Set from GENCODE Version 27 (Ensembl 90) Comprehensive Gene Annotation Set from GENCODE Version 27 (Ensembl 90) Basic Gene Annotation Set from GENCODE Version 27 (Ensembl 90) 2-way Pseudogene Annotation Set from GENCODE Version 27 (Ensembl 90) PolyA Transcript Annotation Set from GENCODE Version 26 (Ensembl 88) Pseudogene Annotation Set from GENCODE Version 26 (Ensembl 88) Comprehensive Gene Annotation Set from GENCODE Version 26 (Ensembl 88) Basic Gene Annotation Set from GENCODE Version 26 (Ensembl 88) 2-way Pseudogene Annotation Set from GENCODE Version 26 (Ensembl 88) PolyA Transcript Annotation Set from GENCODE Version 25 (Ensembl 85) Pseudogene Annotation Set from GENCODE Version 25 (Ensembl 85) Comprehensive Gene Annotation Set from GENCODE Version 25 (Ensembl 85) Basic Gene Annotation Set from GENCODE Version 25 (Ensembl 85) 2-way Pseudogene Annotation Set from GENCODE Version 25 (Ensembl 85) PolyA Transcript Annotation Set from GENCODE Version 24 (Ensembl 83) Pseudogene Annotation Set from GENCODE Version 24 (Ensembl 83) Comprehensive Gene Annotation Set from GENCODE Version 24 (Ensembl 83) Basic Gene Annotation Set from GENCODE Version 24 (Ensembl 83) 2-way Pseudogene Annotation Set from GENCODE Version 24 (Ensembl 83) PolyA Transcript Annotation Set from GENCODE Version 23 (Ensembl 81) Pseudogene Annotation Set from GENCODE Version 23 (Ensembl 81) Comprehensive Gene Annotation Set from GENCODE Version 23 (Ensembl 81) Basic Gene Annotation Set from GENCODE Version 23 (Ensembl 81) 2-way Pseudogene Annotation Set from GENCODE Version 23 (Ensembl 81) PolyA Transcript Annotation Set from GENCODE Version 22 (Ensembl 79) Pseudogene Annotation Set from GENCODE Version 22 (Ensembl 79) Comprehensive Gene Annotation Set from GENCODE Version 22 (Ensembl 79) Basic Gene Annotation Set from GENCODE Version 22 (Ensembl 79) 2-way Pseudogene Annotation Set from GENCODE Version 22 (Ensembl 79) PolyA Transcript Annotation Set from GENCODE Version 20 (Ensembl 76) Pseudogene Annotation Set from GENCODE Version 20 (Ensembl 76) Comprehensive Gene Annotation Set from GENCODE Version 20 (Ensembl 76) Basic Gene Annotation Set from GENCODE Version 20 (Ensembl 76) 2-way Pseudogene Annotation Set from GENCODE Version 20 (Ensembl 76) AUGUSTUS ab initio gene predictions v3.1 Consensus CDS ncORFs: GENCODE Phase II non-canonical ORFs - comprehensive ncORFs: GENCODE Phase II non-canonical ORFs - primary Geneid Gene Predictions Genscan Gene Predictions lincRNA and TUCP transcripts MANE Select Plus Clinical: Representative transcript from RefSeq & GENCODE ncORFs: MetamORF - meta-database of non-canonical ORFs ncORFs: nuORFdb - non-canonical ORFs from nuORFdb v1.2 ncORFs: OpenProt - alternative and reference proteins v2.2 ncORFs: OpenProt - proteins with at least 2 MS peptides v2.2 Non-Human RefSeq Genes SGP Gene Predictions Using Mouse/Human Homology Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs ncORFs: Upstream Open Reading Frames (uORFs) from UTRannotator

The annotations in this section provide predicted regulatory regions based on various experimental data. When a variant overlaps an annotation selected here, the consequence term regulatory_region_variant will be assigned. Follow the links to description pages that explain how each dataset was constructed. Some datasets cover a significant portion of the genome and it may be desirable to filter these annotations by cell type and/or score in order to avoid an overabundance of hits.

DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)  filter items minimum peak score [0-1000]:

Database of Non-synonymous Functional Predictions (dbNSFP)
dbNSFP (Liu et al. 2015) release 3.1a provides pre-computed scores and predictions of functional significance from a variety of tools. Every possible coding change to transcripts in Gencode release 22 (Ensembl 79, Mar. 2015) gene predictions has been evaluated. Note: This may not encompass all transcripts in your selected gene set. Variant Effect Scoring Tool (VEST) (scores [0-1] predict confidence that a change is deleterious SIFT (D = damaging, T = tolerated) PolyPhen-2 with HumDiv training set (D = probably damaging, P = possibly damaging, B = benign) PolyPhen-2 with HumVar training set (D = probably damaging, P = possibly damaging, B = benign) MutationTaster (A = disease causing automatic, D = disease causing, N = polymorphism, P = polymorphism automatic) MutationAssessor (high or medium: predicted functional; low or neutral: predicted non-functional) Likelihood ratio test (LRT) (D = deleterious, N = Neutral, U = unknown) InterPro protein domains GERP++ Rejected Substitutions (RS) GERP++ Neutral Rate (NR)
Transcript status