Variant report

Variant	rs71358887
Chromosome Location	chr19:53100999-53101000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-2	chr19:53100952-53101356	ENSG00000268970.1

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16984003	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34202608	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34281921	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35217466	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35265503	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35443353	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35496699	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35512045	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv963070	chr19:53091108-53105222	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	esv1827275	chr19:53099297-53103875	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
2	chr19:53087400-53103600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:53087600-53103600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:53088400-53103600	Weak transcription	Psoas Muscle	Psoas
5	chr19:53088800-53103600	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:53088800-53103600	Weak transcription	Right Ventricle	heart
7	chr19:53088800-53103800	Weak transcription	Right Atrium	heart
8	chr19:53089000-53103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:53091000-53104200	Weak transcription	Spleen	Spleen
10	chr19:53092200-53103600	Weak transcription	Gastric	stomach
11	chr19:53094000-53103800	Weak transcription	Aorta	Aorta
12	chr19:53095000-53103400	Weak transcription	Fetal Heart	heart
13	chr19:53096000-53103600	Weak transcription	Pancreas	Pancrea
14	chr19:53096000-53103800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:53096000-53104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:53096600-53102200	ZNF genes & repeats	Fetal Intestine Large	intestine
17	chr19:53097600-53101000	Strong transcription	Dnd41	blood
18	chr19:53097600-53101200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:53097600-53101200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
20	chr19:53097600-53101200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:53097600-53102200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:53097800-53101000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr19:53097800-53102800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:53098000-53101000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:53098000-53101200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:53098200-53101000	Strong transcription	Fetal Muscle Leg	muscle
27	chr19:53098200-53103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:53098600-53101200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr19:53099200-53101000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
30	chr19:53099200-53101200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:53099400-53101000	ZNF genes & repeats	NHEK	skin
32	chr19:53099400-53101200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:53099400-53101200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:53099400-53101200	Strong transcription	Brain Germinal Matrix	brain
35	chr19:53099400-53101800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:53099400-53103400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:53099600-53101000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr19:53099600-53101400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:53099600-53103600	Weak transcription	Brain Anterior Caudate	brain
40	chr19:53099600-53104000	Weak transcription	Ovary	ovary
41	chr19:53099800-53101200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:53099800-53103600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:53100000-53102200	Strong transcription	Fetal Brain Female	brain
44	chr19:53100000-53103400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:53100000-53103400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr19:53100000-53103600	Weak transcription	Brain Angular Gyrus	brain
47	chr19:53100000-53103600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:53100000-53103600	Weak transcription	Left Ventricle	heart
49	chr19:53100000-53103600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:53100000-53103600	Weak transcription	NHLF	lung

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