Variant report

Variant	rs61742743
Chromosome Location	chr9:16626240-16626241
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTLN-3	chr9:16626156-16626388	ENSG00000230694.1

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7040078	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16611400-16626400	Weak transcription	Aorta	Aorta
2	chr9:16622400-16626600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr9:16622400-16628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:16622400-16628600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:16622400-16628800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:16622600-16626400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:16622600-16628600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:16623200-16628000	Enhancers	Fetal Lung	lung
9	chr9:16623800-16626600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:16624000-16628200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:16624200-16626400	Enhancers	Rectal Smooth Muscle	rectum
12	chr9:16624200-16626400	Enhancers	NHDF-Ad	bronchial
13	chr9:16624200-16626600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:16624200-16627600	Enhancers	Dnd41	blood
15	chr9:16624200-16629000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:16624200-16629200	Enhancers	Fetal Stomach	stomach
17	chr9:16624200-16630400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:16624400-16626400	Enhancers	Stomach Smooth Muscle	stomach
19	chr9:16624400-16627800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:16624400-16628800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr9:16624600-16628800	Enhancers	Fetal Kidney	kidney
22	chr9:16624800-16626600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:16624800-16628600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr9:16624800-16628800	Enhancers	Fetal Thymus	thymus
25	chr9:16625000-16626600	Enhancers	HSMM	muscle
26	chr9:16625000-16626800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:16625000-16628400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:16625000-16630000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:16625200-16626800	Flanking Active TSS	NHLF	lung
30	chr9:16625200-16627800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:16625400-16626800	Enhancers	Psoas Muscle	Psoas
32	chr9:16625400-16627200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:16625400-16627200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:16625400-16627400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr9:16625400-16627800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:16625600-16626600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:16625600-16626600	Weak transcription	Brain Germinal Matrix	brain
38	chr9:16625600-16626600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:16625600-16626800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr9:16625600-16627000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:16625600-16627000	Flanking Active TSS	NH-A	brain
42	chr9:16625600-16627200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr9:16625600-16627200	Bivalent Enhancer	Fetal Heart	heart
44	chr9:16625600-16629000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:16625800-16626600	Weak transcription	Adipose Nuclei	Adipose
46	chr9:16625800-16626800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:16625800-16626800	Weak transcription	Right Atrium	heart
48	chr9:16625800-16627200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:16625800-16627200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr9:16625800-16627600	Flanking Active TSS	HSMMtube	muscle

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