Variant report

Variant	rs12572769
Chromosome Location	chr10:43306974-43306975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RET-4	chr10:43306923-43307499	l_299_chr10:43299976-43307499_brain

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1008751	0.80[AMR][1000 genomes]
rs10900276	0.82[AMR][1000 genomes]
rs11239781	0.82[AMR][1000 genomes]
rs11239784	0.82[AMR][1000 genomes]
rs11239785	0.82[AMR][1000 genomes]
rs11239787	0.82[AMR][1000 genomes]
rs1539293	0.80[AMR][1000 genomes]
rs1539294	0.80[AMR][1000 genomes]
rs3982211	0.80[AMR][1000 genomes]
rs4949035	0.81[AMR][1000 genomes]
rs6593496	0.82[AMR][1000 genomes]
rs6593498	0.82[AMR][1000 genomes]
rs6593499	0.82[AMR][1000 genomes]
rs7069774	0.82[AMR][1000 genomes]
rs7894010	0.81[AMR][1000 genomes]
rs7895230	0.82[AMR][1000 genomes]
rs7909445	0.81[AMR][1000 genomes]
rs7922559	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv895076	chr10:43234432-43326627	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv947891	chr10:43299039-43319274	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv14695	chr10:43301539-43355457	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43279800-43307600	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr10:43279800-43307800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr10:43279800-43307800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:43279800-43308400	Strong transcription	Fetal Intestine Large	intestine
5	chr10:43279800-43308800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:43279800-43309000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr10:43279800-43324000	Strong transcription	Liver	Liver
8	chr10:43279800-43328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:43280000-43309600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:43280000-43310800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:43280200-43310600	Strong transcription	Primary T cells from cord blood	blood
12	chr10:43281000-43308600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:43282400-43308200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr10:43293000-43307600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:43293200-43332400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr10:43294400-43311800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:43294600-43322800	Weak transcription	Stomach Mucosa	stomach
18	chr10:43295000-43308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:43295000-43309400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:43295600-43311800	Weak transcription	Pancreas	Pancrea
21	chr10:43296600-43307600	Weak transcription	Aorta	Aorta
22	chr10:43296600-43307600	Weak transcription	Spleen	Spleen
23	chr10:43296600-43307800	Weak transcription	Esophagus	oesophagus
24	chr10:43296600-43309400	Weak transcription	Small Intestine	intestine
25	chr10:43296800-43311800	Weak transcription	Colonic Mucosa	Colon
26	chr10:43297800-43307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr10:43298800-43313000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:43299600-43309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr10:43299600-43309600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr10:43299600-43318600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr10:43299800-43309200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr10:43299800-43312400	Weak transcription	HSMMtube	muscle
33	chr10:43299800-43313000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr10:43300000-43312800	Weak transcription	Fetal Brain Male	brain
35	chr10:43300000-43318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:43300800-43310600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:43301200-43308200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:43301200-43309200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:43301600-43323000	Weak transcription	HMEC	breast
40	chr10:43301800-43318000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:43301800-43325800	Weak transcription	NHLF	lung
42	chr10:43302000-43311400	Weak transcription	HepG2	liver
43	chr10:43302600-43312800	Weak transcription	Fetal Kidney	kidney
44	chr10:43302800-43309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:43302800-43313000	Weak transcription	Brain Hippocampus Middle	brain
46	chr10:43303000-43307000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:43303000-43307200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr10:43303000-43307400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr10:43303000-43307600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:43303000-43307600	Weak transcription	Lung	lung

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