Variant report

Variant	rs7254868
Chromosome Location	chr19:53101207-53101208
allele	C/T
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: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10403603	0.91[ASN][1000 genomes]
rs10417933	0.81[AFR][1000 genomes]
rs10419118	0.88[AMR][1000 genomes]
rs10420776	0.91[ASN][1000 genomes]
rs11672999	0.91[ASN][1000 genomes]
rs11878446	0.89[ASN][1000 genomes]
rs11880926	0.91[ASN][1000 genomes]
rs11880939	0.90[ASN][1000 genomes]
rs11882538	0.96[ASN][1000 genomes]
rs11882556	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11883366	0.91[ASN][1000 genomes]
rs12979546	0.91[ASN][1000 genomes]
rs12985245	0.90[ASN][1000 genomes]
rs1802617	0.93[ASN][1000 genomes]
rs2068066	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2068067	0.91[ASN][1000 genomes]
rs2068068	0.91[ASN][1000 genomes]
rs2126501	0.96[ASN][1000 genomes]
rs2169527	0.87[ASN][1000 genomes]
rs2169528	0.87[ASN][1000 genomes]
rs2279151	0.91[ASN][1000 genomes]
rs2279152	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs329973	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs35151776	0.91[ASN][1000 genomes]
rs35379780	0.87[ASN][1000 genomes]
rs4450518	0.95[ASN][1000 genomes]
rs4801920	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4801921	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4801922	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801923	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4802975	0.91[ASN][1000 genomes]
rs4802976	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60763836	0.90[ASN][1000 genomes]
rs62117255	0.91[ASN][1000 genomes]
rs62117256	0.91[ASN][1000 genomes]
rs6509653	0.89[ASN][1000 genomes]
rs6509654	0.90[ASN][1000 genomes]
rs6509655	0.91[ASN][1000 genomes]
rs67036527	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7245397	0.96[ASN][1000 genomes]
rs7247002	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7247069	0.91[ASN][1000 genomes]
rs7250819	0.89[ASN][1000 genomes]
rs7259768	0.96[ASN][1000 genomes]
rs7259905	0.90[ASN][1000 genomes]
rs7259938	0.90[ASN][1000 genomes]
rs7260122	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs7260315	0.89[ASN][1000 genomes]
rs74176156	0.90[ASN][1000 genomes]
rs8106002	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110686	0.87[ASN][1000 genomes]
rs8110794	0.87[ASN][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:92 , 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	chr19:53097600-53102200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:53097800-53102800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:53098200-53103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:53099400-53101800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:53099400-53103400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:53099600-53101400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:53099600-53103600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:53099600-53104000	Weak transcription	Ovary	ovary
25	chr19:53099800-53103600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr19:53100000-53102200	Strong transcription	Fetal Brain Female	brain
27	chr19:53100000-53103400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:53100000-53103400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr19:53100000-53103600	Weak transcription	Brain Angular Gyrus	brain
30	chr19:53100000-53103600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:53100000-53103600	Weak transcription	Left Ventricle	heart
32	chr19:53100000-53103600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:53100000-53103600	Weak transcription	NHLF	lung
34	chr19:53100000-53103800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:53100000-53103800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:53100000-53104200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:53100200-53103200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:53100200-53103400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:53100200-53103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:53100200-53103400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:53100200-53103400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:53100200-53103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:53100200-53103400	Weak transcription	NHDF-Ad	bronchial
44	chr19:53100200-53103600	Weak transcription	Brain Hippocampus Middle	brain
45	chr19:53100200-53103600	Weak transcription	HUVEC	blood vessel
46	chr19:53100200-53103800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:53100200-53103800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:53100400-53103000	Weak transcription	Fetal Lung	lung
49	chr19:53100400-53103200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:53100400-53103400	Weak transcription	Rectal Mucosa Donor 29	rectum

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