Variant report

Variant	rs2928188
Chromosome Location	chr19:21555850-21555851
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: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1114305	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875256	0.99[ASN][1000 genomes]
rs2086319	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434996	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562402	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562409	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562415	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562438	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2650797	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650842	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650849	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650851	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs279804	0.86[EUR][1000 genomes]
rs279805	0.86[EUR][1000 genomes]
rs279810	0.86[EUR][1000 genomes]
rs279811	0.86[EUR][1000 genomes]
rs279812	0.86[EUR][1000 genomes]
rs279814	0.86[EUR][1000 genomes]
rs279815	0.86[EUR][1000 genomes]
rs279816	0.86[EUR][1000 genomes]
rs279819	0.83[EUR][1000 genomes]
rs279820	0.86[EUR][1000 genomes]
rs2914626	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914627	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914635	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2914645	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928209	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928211	0.90[ASN][1000 genomes]
rs2928216	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2928218	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937157	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937174	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968022	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968023	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968024	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2968040	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2968041	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968045	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968046	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2968066	0.93[EUR][1000 genomes]
rs2968082	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2968086	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs472472	0.93[EUR][1000 genomes]
rs475162	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476376	0.86[EUR][1000 genomes]
rs478046	0.86[EUR][1000 genomes]
rs487991	0.93[EUR][1000 genomes]
rs489613	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs489845	0.93[EUR][1000 genomes]
rs492271	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs499445	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs501563	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs504026	0.86[EUR][1000 genomes]
rs508656	0.86[EUR][1000 genomes]
rs511469	0.86[EUR][1000 genomes]
rs527060	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537114	0.86[EUR][1000 genomes]
rs540637	0.86[EUR][1000 genomes]
rs540714	0.86[EUR][1000 genomes]
rs541639	0.86[EUR][1000 genomes]
rs547516	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs555596	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs583680	0.86[EUR][1000 genomes]
rs586144	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs598959	0.93[EUR][1000 genomes]
rs600186	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609806	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612877	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627522	0.84[ASN][1000 genomes]
rs631436	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651454	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661453	0.86[EUR][1000 genomes]
rs8102235	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8112775	0.93[EUR][1000 genomes]
rs924485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][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:119 , 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	chr19:21544400-21556200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:21547800-21557000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:21548000-21556600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr19:21549000-21556600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:21549000-21560600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:21549800-21560400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr19:21550000-21556200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:21550200-21559200	Strong transcription	Ovary	ovary
37	chr19:21550800-21562200	Weak transcription	Brain Angular Gyrus	brain
38	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:21551200-21556600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:21551600-21561800	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:21552000-21560400	Strong transcription	Fetal Lung	lung
42	chr19:21552000-21563200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
43	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
44	chr19:21552200-21560200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:21552200-21561400	Weak transcription	Esophagus	oesophagus
46	chr19:21552400-21559400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:21552600-21556600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:21552800-21559200	Weak transcription	Lung	lung
49	chr19:21552800-21561400	Weak transcription	Aorta	Aorta
50	chr19:21553400-21557000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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