Variant report

Variant	rs55771551
Chromosome Location	chr19:21746380-21746381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-3	chr19:21744136-21747283	XLOC_013263

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10420016	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10854048	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10854050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10854051	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11085462	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085463	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11085465	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11085468	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668606	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671579	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879234	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2173727	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562398	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2562408	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562417	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562466	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562468	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562471	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562507	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2562508	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2650792	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650793	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650804	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650805	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650825	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681370	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681377	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681388	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681389	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681392	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681395	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2946790	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35008138	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35099594	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4809144	0.89[AFR][1000 genomes]
rs4809145	0.89[AFR][1000 genomes]
rs58001930	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60206762	0.89[AFR][1000 genomes]
rs62110163	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62110202	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110205	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110214	0.89[AFR][1000 genomes]
rs6511253	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511254	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511256	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511258	0.85[ASN][1000 genomes]
rs7259708	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9304986	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304987	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
5	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
6	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
7	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS 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
11	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv963025	chr19:21742797-21754765	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv828496	chr19:21745795-21766943	Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs55771551	ZNF708	cis	lung	GTEx
rs55771551	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs55771551	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs55771551	ZNF708	cis	Muscle Skeletal	GTEx
rs55771551	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs55771551	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21737200-21747200	ZNF genes & repeats	Fetal Intestine Small	intestine
2	chr19:21738000-21749400	Weak transcription	Left Ventricle	heart
3	chr19:21738000-21751400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:21738600-21751600	Weak transcription	Osteobl	bone
5	chr19:21738800-21746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:21739400-21751200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr19:21740200-21746400	ZNF genes & repeats	Fetal Intestine Large	intestine
8	chr19:21740600-21750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:21742800-21750600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:21743000-21746400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:21743200-21750400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:21743600-21751600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:21744200-21747000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
14	chr19:21744800-21746600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:21744800-21747600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:21744800-21750600	Weak transcription	Colonic Mucosa	Colon
17	chr19:21744800-21750600	Weak transcription	Fetal Kidney	kidney
18	chr19:21745000-21750600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:21745200-21746600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:21745200-21749400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:21745800-21746800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:21745800-21747200	Strong transcription	Fetal Stomach	stomach
23	chr19:21745800-21748000	Strong transcription	Dnd41	blood
24	chr19:21746000-21746600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:21746000-21746600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:21746000-21746600	Strong transcription	Adipose Nuclei	Adipose
27	chr19:21746000-21746600	ZNF genes & repeats	Fetal Brain Male	brain
28	chr19:21746000-21746600	ZNF genes & repeats	Lung	lung
29	chr19:21746000-21746600	ZNF genes & repeats	Ovary	ovary
30	chr19:21746000-21746600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr19:21746000-21746800	ZNF genes & repeats	Liver	Liver
32	chr19:21746000-21746800	Strong transcription	Fetal Lung	lung
33	chr19:21746000-21746800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
34	chr19:21746000-21747000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr19:21746000-21747600	Strong transcription	Primary T cells from cord blood	blood
36	chr19:21746200-21746400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:21746200-21746600	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr19:21746200-21746600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr19:21746200-21746600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr19:21746200-21746800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr19:21746200-21746800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr19:21746200-21747000	ZNF genes & repeats	Thymus	Thymus

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