Variant report

Variant	rs2650838
Chromosome Location	chr19:21555269-21555270
allele	A/G
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: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10410362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10412054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11878543	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11879647	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11880701	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11880751	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11881331	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11881379	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11882304	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1762561	1.00[AMR][1000 genomes]
rs1762562	1.00[AMR][1000 genomes]
rs1762569	1.00[AMR][1000 genomes]
rs1781849	1.00[AMR][1000 genomes]
rs1781854	1.00[AMR][1000 genomes]
rs1781859	1.00[AMR][1000 genomes]
rs1846713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1909772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1963057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2011379	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2088759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2173726	1.00[AMR][1000 genomes]
rs2359147	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2359148	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2434998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2454922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2537693	1.00[AMR][1000 genomes]
rs2537695	1.00[AMR][1000 genomes]
rs2562412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2562434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2650811	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2650839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2801860	1.00[AMR][1000 genomes]
rs28857324	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2914643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2914644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2928219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2928220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968071	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35464445	1.00[ASN][1000 genomes]
rs57626552	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57847044	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58638125	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59087535	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59268487	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61062763	1.00[ASN][1000 genomes]
rs61334868	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7249229	1.00[AMR][1000 genomes]
rs73539807	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73543709	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73545768	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73545790	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73549716	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8112786	1.00[AMR][1000 genomes];1.00[ASN][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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21542400-21555400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr19:21542400-21555400	Weak transcription	Psoas Muscle	Psoas
3	chr19:21542400-21555600	Weak transcription	Colonic Mucosa	Colon
4	chr19:21542400-21557800	Weak transcription	Gastric	stomach
5	chr19:21542400-21562200	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:21542400-21562200	Weak transcription	Fetal Heart	heart
7	chr19:21542400-21563200	Weak transcription	Brain Substantia Nigra	brain
8	chr19:21542600-21555600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:21542600-21561400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:21542600-21561400	Weak transcription	Pancreas	Pancrea
11	chr19:21542800-21561400	Weak transcription	Right Ventricle	heart
12	chr19:21543000-21555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:21543000-21556600	Weak transcription	HepG2	liver
14	chr19:21543000-21563000	Weak transcription	NHLF	lung
15	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:21543200-21555400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:21543200-21555800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:21543200-21556600	ZNF genes & repeats	GM12878-XiMat	blood
20	chr19:21543200-21557000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:21543400-21555400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:21543400-21560000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr19:21543400-21560400	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr19:21543600-21563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:21543800-21556800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:21544200-21560400	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr19:21544200-21561400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:21544400-21556200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr19:21547800-21557000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:21548000-21556600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr19:21548400-21555400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:21548800-21555800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:21549000-21556600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr19:21549000-21560600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:21549400-21555600	Weak transcription	A549	lung
45	chr19:21549800-21560400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr19:21550000-21556200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:21550200-21555400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:21550200-21559200	Strong transcription	Ovary	ovary
49	chr19:21550800-21555400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:21550800-21562200	Weak transcription	Brain Angular Gyrus	brain

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