Variant report

Variant	rs17272889
Chromosome Location	chr19:53684222-53684223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF665-1	chr19:53683900-53686196	NONHSAT067645

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16984547	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS 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 target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
9	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv912350	chr19:53636016-53687818	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv912351	chr19:53655493-53702508	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv2762999	chr19:53665818-53709353	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1065473	chr19:53680455-53709341	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	22 gene(s)	inside rSNPs	diseases
16	nsv458761	chr19:53682042-53705554	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv458763	chr19:53682042-53705554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv458764	chr19:53682042-53705554	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv458765	chr19:53682042-53705554	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv458766	chr19:53682042-53705554	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv580078	chr19:53682042-53705554	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1060349	chr19:53682042-53709341	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53664800-53695400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:53669400-53685800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:53669400-53695600	Weak transcription	Brain Germinal Matrix	brain
4	chr19:53670000-53695400	Weak transcription	Right Ventricle	heart
5	chr19:53670200-53695200	Weak transcription	Fetal Brain Female	brain
6	chr19:53672200-53686400	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:53673600-53688200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:53674000-53695400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:53674000-53695600	Weak transcription	Brain Angular Gyrus	brain
10	chr19:53674000-53695600	Weak transcription	Brain Anterior Caudate	brain
11	chr19:53674200-53693600	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:53674200-53693600	Weak transcription	Fetal Muscle Leg	muscle
13	chr19:53676600-53693600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:53677200-53685800	Weak transcription	Fetal Stomach	stomach
15	chr19:53677400-53685000	Weak transcription	Placenta	Placenta
16	chr19:53677600-53686400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:53677600-53695600	Weak transcription	Fetal Lung	lung
18	chr19:53678800-53695800	Weak transcription	Aorta	Aorta
19	chr19:53679800-53686600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:53680000-53684800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:53680200-53695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:53680600-53695600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:53681000-53685600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:53681000-53695600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:53681200-53695400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:53681400-53686000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr19:53681400-53693400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:53681400-53695600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:53681600-53685800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:53682000-53685200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr19:53682000-53693600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:53682200-53685800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:53682200-53686000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:53682200-53686000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:53682400-53685400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:53682400-53685800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:53682400-53695400	Weak transcription	NHDF-Ad	bronchial
38	chr19:53682600-53684400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:53682600-53687800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:53682800-53685000	Strong transcription	Osteobl	bone
41	chr19:53682800-53686600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:53682800-53687200	Strong transcription	Dnd41	blood
43	chr19:53682800-53687400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr19:53682800-53688000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr19:53682800-53695600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:53683000-53684800	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:53683000-53685400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:53683000-53686800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:53683200-53685000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:53683200-53685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links