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.
UCSC Genes (RefSeq, GenBank, CCDS, Rfam, tRNAs & Comparative Genomics) 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, curated subset (NM_*, NR_*, NP_* or YP_*) NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) Pseudogene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Comprehensive Gene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Basic Gene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Pseudogene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Comprehensive Gene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Basic Gene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Pseudogene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Comprehensive Gene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Basic Gene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Pseudogene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Comprehensive Gene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Basic Gene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Pseudogene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Comprehensive Gene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Basic Gene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Pseudogene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Comprehensive Gene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Basic Gene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Pseudogene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Comprehensive Gene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Basic Gene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Pseudogene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Comprehensive Gene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Basic Gene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Pseudogene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Comprehensive Gene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Basic Gene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Pseudogene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Comprehensive Gene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Basic Gene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Pseudogene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Comprehensive Gene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Basic Gene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Pseudogene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Comprehensive Gene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Basic Gene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Pseudogene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Comprehensive Gene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Basic Gene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Pseudogene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Comprehensive Gene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Basic Gene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Pseudogene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Comprehensive Gene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Basic Gene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Pseudogene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Comprehensive Gene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Basic Gene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Pseudogene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) Comprehensive Gene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) Basic Gene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) PolyA Transcript Annotation Set from GENCODE Version 19 Pseudogene Annotation Set from GENCODE Version 19 Comprehensive Gene Annotation Set from GENCODE Version 19 Basic Gene Annotation Set from GENCODE Version 19 2-way Pseudogene Annotation Set from GENCODE Version 19 PolyA Transcript Annotation Set from ENCODE/GENCODE Version 17 Pseudogene Annotation Set from ENCODE/GENCODE Version 17 Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 17 Basic Gene Annotation Set from ENCODE/GENCODE Version 17 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 17 PolyA Transcript Annotation Set from ENCODE/GENCODE Version 14 Pseudogene Annotation Set from ENCODE/GENCODE Version 14 Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 14 Basic Gene Annotation Set from ENCODE/GENCODE Version 14 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 14 PolyA Transcript Annotation Set from ENCODE/GENCODE Version 7 Pseudogene Annotation Set from ENCODE/GENCODE Version 7 Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 7 Basic Gene Annotation Set from ENCODE/GENCODE Version 7 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 7 AceView Gene Models With Alt-Splicing AUGUSTUS ab initio gene predictions v3.1 Consensus CDS Ensembl Genes Exoniphy Human/Mouse/Rat/Dog Geneid Gene Predictions Genscan Gene Predictions lincRNA and TUCP transcripts N-SCAN Gene Predictions Previous Version of UCSC Genes Non-Human RefSeq Genes SGP Gene Predictions Using Mouse/Human Homology Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs Vega Annotated Pseudogenes and Immunoglobulin Segments Vega Protein-Coding Annotations Yale Pseudogenes based on Ensembl Release 60

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.

DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)  filter items minimum peak score [0-1000]:

Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs  filter items factor: AllARID3AATF1ATF2ATF3BACH1BATFBCL11ABCL3BCLAF1BDP1BHLHE40BRCA1BRF1BRF2CBX3CCNT2CEBPBCEBPDCHD1CHD2CREB1CTBP2CTCFCTCFLE2F1E2F4E2F6EBF1EGR1ELF1ELK1ELK4EP300ESR1ESRRAETS1EZH2FAM48AFOSFOSL1FOSL2FOXA1FOXA2FOXM1FOXP2GABPAGATA1GATA2GATA3GRp20GTF2BGTF2F1GTF3C2HDAC1HDAC2HDAC6HDAC8HMGN3HNF4AHNF4GHSF1IKZF1IRF1IRF3IRF4JUNJUNBJUNDKAP1KDM5AKDM5BMAFFMAFKMAXMAZMBD4MEF2AMEF2CMTA3MXI1MYBL2MYCNANOGNFATC1NFE2NFICNFYANFYBNR2C2NR2F2NR3C1NRF1PAX5PBX3PHF8PMLPOLR2APOLR3GPOU2F2POU5F1PPARGC1APRDM1RAD21RBBP5RCOR1RDBPRELARESTRFX5RPC155RUNX3RXRASAP30SETDB1SIN3ASIN3AK20SIRT6SIX5SMARCA4SMARCB1SMARCC1SMARCC2SMC3SP1SP2SP4SPI1SREBP1SRFSTAT1STAT2STAT3STAT5ASUZ12TAF1TAF7TAL1TBL1XR1TBPTCF12TCF3TCF7L2TEAD4TFAP2ATFAP2CTHAP1TRIM28UBTFUSF1USF2WRNIP1YY1ZBTB33ZBTB7AZEB1ZKSCAN1ZNF143ZNF217ZNF263ZNF274ZZZ3 cell type: AllA549AG04449AG04450AG09309AG09319AG10803AoAFBE2_CBJCaco-2Dnd41ECC-1FibroblGlioblaGM06990GM08714GM10847GM12801GM12864GM12865GM12872GM12873GM12874GM12875GM12878GM12891GM12892GM15510GM18505GM18526GM18951GM19099GM19193GM19238GM19239GM19240H1-hESCHA-spHAcHBMECHCFaaHCMHCPEpiCHCT-116HEEpiCHEK293HEK293-T-RExHeLa-S3HepG2HFFHFF-MycHL-60HMECHMFHPAFHPFHREHRPEpiCHSMMHSMMtubeHUVECHVMFIMR90K562MCF-7MCF10A-Er-SrcNB4NH-ANHDF-AdNHDF-neoNHEKNHLFNT2-D1OsteoblPANC-1PBDEPBDEFetalPFSK-1ProgFibRajiRPTECSAECSH-SY5YSK-N-MCSK-N-SHSK-N-SH_RAT-47DU2OSU87WERI-Rb-1WI-38 treatment: All4OHTAM_1uM_12hr4OHTAM_1uM_36hr4OHTAM_1uM_4hrBPA_100nMDEX_100nMDEX_500pMDEX_50nMDEX_5nMDMSO_0.02pctEstradiol_10nMestrogenEtOH_0.01pctEtOH_0.01pct_12hrEtOH_0.01pct_4hrEtOH_0.02pctforskolinGenistein_100nMIFNa30IFNa6hIFNg30IFNg6hinsulinMNaseDNoneserum_starved_mediaserum_stimulated_mediaTNFavehicle minimum peak score [0-1000]:

Database of Non-synonymous Functional Predictions (dbNSFP)

dbNSFP (Liu et al. 2013) release 2.0 provides pre-computed scores and predictions of functional significance from a variety of tools. Every possible coding change to transcripts in Gencode release 9 (Ensembl 64, Dec. 2011) gene predictions has been evaluated. Note: This may not encompass all transcripts in your selected gene set. 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

Include the GENCODE tags (if any) associated with each transcript. Indicate whether each transcript is 'canonical' (generally the longest isoform of a gene). Include the RefSeq status of each transcript. No transcript status data are available for the selected gene track.

HGVS variant nomenclature

The Human Genome Variation Society (HGVS) has established a sequence variant nomenclature, an international standard used to report variation in genomic, transcript and protein sequences. Include HGVS genomic (g.) terms in output Include HGVS coding (c.) terms if applicable, otherwise noncoding (n.) terms, in output Include HGVS protein (p.) terms (if applicable) in output When including HGVS protein (p.) terms, add parentheses around changes to emphasize that they are predictions For variants that involve both a deletion and insertion, including multi-nucleotide variants, include the deleted sequence (e.g. show "delAGinsTT" instead of only "delinsTT") Select RefSeq Genes or an official GENCODE release ("Basic Gene Annotation Set from GENCODE..." or "Comprehensive Gene Annotation Set...") in the "Select Genes" section above in order to make options appear.

Known variation

Include dbSNP rs# ID if one exists

Conserved elements

100 vertebrates Conserved Elements Vertebrate Conserved Elements Placental Mammal Conserved Elements Primate Conserved Elements

Conservation scores

100 vertebrates conservation by PhastCons 100 vertebrates Basewise Conservation by PhyloP Vertebrate Conservation by PhastCons Placental Mammal Conservation by PhastCons Primate Conservation by PhastCons Vertebrate Basewise Conservation by PhyloP Placental Mammal Basewise Conservation by PhyloP Primate Basewise Conservation by PhyloP

Functional role

Include variants annotated as intergenic upstream/downstream of gene in transcript already subject to nonsense-mediated decay (NMD) exon loss caused by deletion 5' or 3' UTR CDS - synonymous coding change CDS - non-synonymous (missense, stop gain/loss, frameshift etc) intron splice site or splice region exon of non-coding gene "variants" for which no alternate allele has been observed regulatory element (note: these are detected only if one or more tracks are selected in Regulatory regions above)