# HAO2-IT1 > Gene · canonical: https://sugi.bio/atlas/gene/HAO2-IT1/ > Atlas v1.13.0 · generated 2026-10-14T18:20:41+00:00 ## Summary **HAO2-IT1** (HAO2 intronic transcript 1, HGNC:41342) is a long non-coding RNA gene on chromosome 1p12. **At a glance** - **Gene type:** non-coding (lncRNA) — no protein product. - **GTEx eGene:** eQTL in 2 tissues, sQTL in 0 (q < 0.05) ## Identifiers ### Gene identifiers | Field | Value | | --- | --- | | HGNC ID | HGNC:41342 | | Approved symbol | HAO2-IT1 | | Name | HAO2 intronic transcript 1 | | Location | 1p12 | | Locus type | RNA, long non-coding | | Status | Approved | | Ensembl gene | ENSG00000230921 | | Ensembl biotype | lncRNA | | Entrez | 100874270 | | RNAcentral | URS00005B433E — ncRNA, 311 nt, 2 organism(s) | ## Gene structure ### Transcript identifiers **Ensembl transcripts: 1** — 1 lncRNA **Transcript support level (Ensembl TSL; 1 = fully mRNA-supported):** TSL 5: 1 `ENST00000419144` **RefSeq mRNA: 0** #### Canonical transcript exons `ENST00000419144` — 2 exons | Exon | Start | End | | --- | --- | --- | | ENSE00001614027 | 119368946 | 119369008 | | ENSE00001763846 | 119370084 | 119370331 | ### Expression profiles **Bgee:** expression breadth **broad**, 68 present calls, max score 73.89. **Highest expression (Bgee):** liver, lobe of liver, adrenal gland cortex, adrenal gland, monocyte. #### Genetic regulation across tissues (GTEx eQTL / sQTL) HAO2-IT1 is an **eGene** in GTEx v10 — its expression is genetically regulated (eQTL) in **2** tissues and its splicing (sQTL) in **0** (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant's alternative allele. 2 significant tissue × QTL associations: | Tissue | QTL | q-value | Slope | Lead variant | | --- | --- | --- | --- | --- | | Liver | eqtl | 3.3e-11 | +0.59 | 1:119370216:T:G | | Kidney Cortex | eqtl | 8.9e-03 | +0.70 | 1:119370216:T:G | #### Top tissues by expression 68 tissues by Bgee expression score (0-100, higher = more expressed): | Tissue | Anatomy ID | Expression score | Quality | | --- | --- | --- | --- | | liver | UBERON:0002107 | 73.89 | gold quality | | right lobe of liver | UBERON:0001114 | 71.14 | gold quality | | right adrenal gland cortex | UBERON:0035827 | 66.15 | gold quality | | right adrenal gland | UBERON:0001233 | 65.85 | gold quality | | adrenal gland | UBERON:0002369 | 64.61 | gold quality | | monocyte | CL:0000576 | 64.29 | gold quality | | left adrenal gland | UBERON:0001234 | 64.21 | gold quality | | prefrontal cortex | UBERON:0000451 | 62.81 | gold quality | | left adrenal gland cortex | UBERON:0035825 | 62.68 | gold quality | | blood | UBERON:0000178 | 61.61 | gold quality | | pancreas | UBERON:0001264 | 60.83 | gold quality | | superior frontal gyrus | UBERON:0002661 | 60.51 | gold quality | | body of pancreas | UBERON:0001150 | 60.50 | gold quality | | corpus callosum | UBERON:0002336 | 60.41 | gold quality | | kidney | UBERON:0002113 | 58.34 | gold quality | | adult mammalian kidney | UBERON:0000082 | 57.88 | gold quality | | small intestine | UBERON:0002108 | 57.54 | gold quality | | small intestine Peyer's patch | UBERON:0003454 | 57.49 | gold quality | | cortex of kidney | UBERON:0001225 | 56.09 | gold quality | | Brodmann (1909) area 9 | UBERON:0013540 | 55.33 | gold quality | | intestine | UBERON:0000160 | 54.49 | gold quality | | adenohypophysis | UBERON:0002196 | 54.16 | gold quality | | multicellular organism | UBERON:0000468 | 53.76 | gold quality | | tibial artery | UBERON:0007610 | 53.09 | gold quality | | right ovary | UBERON:0002118 | 51.81 | gold quality | | Ammon's horn | UBERON:0001954 | 51.63 | gold quality | | frontal cortex | UBERON:0001870 | 51.42 | gold quality | | thoracic aorta | UBERON:0001515 | 51.27 | gold quality | | dorsolateral prefrontal cortex | UBERON:0009834 | 51.27 | gold quality | | lower esophagus muscularis layer | UBERON:0035833 | 50.77 | gold quality | | lung | UBERON:0002048 | 50.44 | gold quality | | spleen | UBERON:0002106 | 50.41 | gold quality | | substantia nigra | UBERON:0002038 | 50.02 | gold quality | | esophagus mucosa | UBERON:0002469 | 49.97 | gold quality | | esophagogastric junction muscularis propria | UBERON:0035841 | 49.88 | gold quality | | stomach | UBERON:0000945 | 49.77 | gold quality | | subcutaneous adipose tissue | UBERON:0002190 | 49.70 | gold quality | | right frontal lobe | UBERON:0002810 | 49.68 | gold quality | | brain | UBERON:0000955 | 49.41 | gold quality | | ascending aorta | UBERON:0001496 | 49.36 | gold quality | | muscle layer of sigmoid colon | UBERON:0035805 | 49.14 | gold quality | | rectum | UBERON:0001052 | 49.10 | gold quality | | body of stomach | UBERON:0001161 | 49.08 | gold quality | | heart | UBERON:0000948 | 48.67 | gold quality | | putamen | UBERON:0001874 | 48.29 | gold quality | | prostate gland | UBERON:0002367 | 48.25 | gold quality | | anterior cingulate cortex | UBERON:0009835 | 48.13 | gold quality | | amygdala | UBERON:0001876 | 47.98 | gold quality | | C1 segment of cervical spinal cord | UBERON:0006469 | 47.98 | gold quality | | cerebellar hemisphere | UBERON:0002245 | 47.41 | gold quality | | skin of abdomen | UBERON:0001416 | 47.07 | gold quality | | hypothalamus | UBERON:0001898 | 47.05 | gold quality | | omental fat pad | UBERON:0010414 | 47.01 | gold quality | | right hemisphere of cerebellum | UBERON:0014890 | 46.88 | gold quality | | left ovary | UBERON:0002119 | 46.81 | gold quality | | nucleus accumbens | UBERON:0001882 | 45.90 | gold quality | | transverse colon | UBERON:0001157 | 45.72 | gold quality | | skin of leg | UBERON:0001511 | 45.35 | gold quality | | caudate nucleus | UBERON:0001873 | 44.96 | gold quality | | right lung | UBERON:0002167 | 44.78 | gold quality | | thoracic mammary gland | UBERON:0005200 | 43.70 | gold quality | | pituitary gland | UBERON:0000007 | 43.58 | gold quality | | tibial nerve | UBERON:0001323 | 42.85 | silver quality | | right atrium auricular region | UBERON:0006631 | 42.30 | silver quality | | vagina | UBERON:0000996 | 42.26 | silver quality | | left lobe of thyroid gland | UBERON:0001120 | 42.11 | silver quality | | metanephros cortex | UBERON:0010533 | 39.77 | silver quality | | left testis | UBERON:0004533 | 26.61 | silver quality | #### Single-cell (SCXA) Detected in 1 experiment(s), a significant marker in 0. | Experiment | Marker? | Max mean expression | | --- | --- | --- | | [E-ANND-3](https://www.ebi.ac.uk/gxa/sc/experiments/E-ANND-3) | no | 1.63 | ### Regulation **Is transcription factor: no** ### Cross-species orthologs **0 orthologs** ### Genomic neighbors (locus context) Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that). | Symbol | Type | Entrez | | --- | --- | --- | | [WARS2](/atlas/gene/WARS2/) | protein-coding | 10352 | | [LINC01780](/atlas/gene/LINC01780/) | ncRNA | 105378934 | | [HAO2](/atlas/gene/HAO2/) | protein-coding | 51179 | | [WARS2-AS1](/atlas/gene/WARS2-AS1/) | ncRNA | 101929147 | | [HSD3B2](/atlas/gene/HSD3B2/) | protein-coding | 3284 | ## Protein *Non-coding RNA — no protein product.* ## Function ### Gene-set membership (MSigDB) This non-coding RNA is a member of 3 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data). `chr1p12`, `MAFG_TARGET_GENES`, `CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN` ### ncRNA interactions Experimentally supported non-coding-RNA interaction partners (NPInter). 2 interaction partners: | Partner | Partner type | Level | Source | | --- | --- | --- | --- | | [FBL](/atlas/gene/FBL/) | protein | RNA-Protein | GSE77027 | | [KHDRBS2](/atlas/gene/KHDRBS2/) | protein | RNA-Protein | High-throughput data | ## Disease & clinical *No curated disease, variant, or cancer-driver associations.* ## Drugs & pharmacology ### ncRNA–drug associations Curated non-coding-RNA → drug associations (drug response / resistance / target). 1 ncRNA–drug associations: | Drug | Relation | Effect | Condition | | --- | --- | --- | --- | | [Gemcitabine](/atlas/drug/gemcitabine/) | drug_resistance | sensitive | cell line (SNU-245) | ## Related Atlas pages - **Associated drugs (ncRNA: response / resistance):** [Gemcitabine](/atlas/drug/gemcitabine/)