Variant report

Variant	rs11670868
Chromosome Location	chr19:21556415-21556416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-6	chr19:21555198-21557246	ucscGeneNc_uc002nqf_1

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10414834	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10424079	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11666213	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11666525	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11666540	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11667103	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11667361	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11667392	0.82[EUR][1000 genomes]
rs11669033	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11669790	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670815	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11672583	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11673320	0.85[AMR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13346641	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1621154	0.88[EUR][1000 genomes]
rs1626404	0.88[EUR][1000 genomes]
rs1762578	0.88[EUR][1000 genomes]
rs17680605	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1781867	0.88[EUR][1000 genomes]
rs1781872	0.88[EUR][1000 genomes]
rs1967182	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2061916	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2154302	0.86[EUR][1000 genomes]
rs2358993	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2359144	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2562405	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562416	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650776	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650844	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650848	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs279807	0.83[EUR][1000 genomes]
rs279809	0.84[EUR][1000 genomes]
rs3853837	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3853838	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321312	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4327181	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4359573	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4544364	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4638726	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55756795	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55875743	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55899865	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57299552	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58412280	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60173523	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61035285	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107465	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62107469	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62107472	0.88[EUR][1000 genomes]
rs62107479	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107531	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107534	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107536	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62107539	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62107540	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62107541	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62109225	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62109226	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62109227	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109228	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109229	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110071	0.84[EUR][1000 genomes]
rs62110367	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110377	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62110416	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110420	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110424	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110426	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110427	0.85[AMR][1000 genomes]
rs62110428	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62110429	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7246339	0.88[EUR][1000 genomes]
rs7251135	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258099	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7258473	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258562	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73537884	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
8	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11670868	ZNF708	cis	Muscle Skeletal	GTEx
rs11670868	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11670868	RP11-678G14.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21542400-21557800	Weak transcription	Gastric	stomach
2	chr19:21542400-21562200	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:21542400-21562200	Weak transcription	Fetal Heart	heart
4	chr19:21542400-21563200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:21542600-21561400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:21542600-21561400	Weak transcription	Pancreas	Pancrea
7	chr19:21542800-21561400	Weak transcription	Right Ventricle	heart
8	chr19:21543000-21556600	Weak transcription	HepG2	liver
9	chr19:21543000-21563000	Weak transcription	NHLF	lung
10	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:21543200-21556600	ZNF genes & repeats	GM12878-XiMat	blood
13	chr19:21543200-21557000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:21543400-21560000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:21543400-21560400	ZNF genes & repeats	Fetal Brain Female	brain
16	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:21543600-21563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:21543800-21556800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:21544200-21560400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr19:21544200-21561400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr19:21547800-21557000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
29	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:21548000-21556600	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr19:21549000-21556600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:21549000-21560600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:21549800-21560400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr19:21550200-21559200	Strong transcription	Ovary	ovary
35	chr19:21550800-21562200	Weak transcription	Brain Angular Gyrus	brain
36	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:21551200-21556600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:21551600-21561800	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:21552000-21560400	Strong transcription	Fetal Lung	lung
40	chr19:21552000-21563200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr19:21552200-21560200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:21552200-21561400	Weak transcription	Esophagus	oesophagus
44	chr19:21552400-21559400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:21552600-21556600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:21552800-21559200	Weak transcription	Lung	lung
47	chr19:21552800-21561400	Weak transcription	Aorta	Aorta
48	chr19:21553400-21557000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:21553600-21557000	ZNF genes & repeats	Thymus	Thymus
50	chr19:21553600-21558000	Strong transcription	Rectal Mucosa Donor 29	rectum

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