Variant report

Variant	rs1879234
Chromosome Location	chr19:21704479-21704480
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-11	chr19:21704145-21704698	NONHSAT063722

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10420016	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854048	0.84[ASN][1000 genomes]
rs10854050	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10854051	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11085462	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11085463	0.80[ASN][1000 genomes]
rs11085465	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11085468	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1114305	0.93[CHB][hapmap]
rs11668606	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11671579	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12974758	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13346641	0.81[CEU][hapmap]
rs1967182	0.86[CEU][hapmap]
rs2086319	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2173727	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359144	0.85[CEU][hapmap]
rs2359155	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562398	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562402	0.93[CHB][hapmap]
rs2562408	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562417	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562435	0.85[CHB][hapmap]
rs2562456	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562471	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562507	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562508	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2650784	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650792	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2650793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2650798	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2650804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2650805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2650825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650844	0.84[CEU][hapmap]
rs2681370	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2681377	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681388	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2681389	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681391	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681392	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681395	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914626	0.93[CHB][hapmap]
rs2914645	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2914646	0.92[AFR][1000 genomes]
rs2928218	0.90[CHB][hapmap]
rs2937174	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2946790	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968045	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2968046	0.93[CHB][hapmap]
rs2968082	0.93[CHB][hapmap]
rs35008138	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35099594	0.81[EUR][1000 genomes]
rs4321312	1.00[CEU][hapmap]
rs4359573	1.00[CEU][hapmap]
rs4638726	0.86[CEU][hapmap]
rs4809145	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs55771551	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58001930	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109226	0.83[AFR][1000 genomes]
rs62109227	0.83[AFR][1000 genomes]
rs62109228	0.83[AFR][1000 genomes]
rs62110163	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511250	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6511254	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6511256	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511258	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252254	0.81[JPT][hapmap]
rs7252585	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259708	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7260065	0.95[CEU][hapmap]
rs8110814	0.81[JPT][hapmap]
rs924485	0.81[JPT][hapmap]
rs9304986	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	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
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1879234	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs1879234	ZNF708	cis	lung	GTEx
rs1879234	ZNF708	cis	Muscle Skeletal	GTEx
rs1879234	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs1879234	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs1879234	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1879234	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21698400-21710800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:21699400-21705400	ZNF genes & repeats	Dnd41	blood
3	chr19:21699600-21707600	ZNF genes & repeats	Brain Germinal Matrix	brain
4	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
6	chr19:21700600-21707800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
7	chr19:21700600-21707800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:21700800-21705400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr19:21700800-21706600	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr19:21700800-21706800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:21700800-21707200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:21700800-21711000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr19:21701000-21704600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr19:21701000-21705200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr19:21701000-21706200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
16	chr19:21701000-21707000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:21701000-21707800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:21701400-21705000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:21701400-21707000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr19:21701400-21707200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:21701400-21707600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr19:21701400-21707600	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:21701400-21708000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:21701600-21704600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr19:21701600-21704600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:21701600-21705000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:21701600-21705000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:21701600-21705400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:21701600-21706200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr19:21701600-21706400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:21701600-21706800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr19:21701600-21707200	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr19:21701600-21707200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
35	chr19:21701600-21712600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:21701600-21720400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr19:21702400-21721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:21702600-21706200	Weak transcription	NH-A	brain
39	chr19:21702600-21713400	Weak transcription	Right Ventricle	heart
40	chr19:21702600-21713400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:21702600-21717200	Weak transcription	Psoas Muscle	Psoas
42	chr19:21702800-21704600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:21702800-21704600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:21702800-21707200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:21702800-21713400	Weak transcription	Brain Angular Gyrus	brain
46	chr19:21702800-21717200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:21702800-21718600	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:21702800-21718600	Weak transcription	Fetal Heart	heart
49	chr19:21703000-21704600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:21703000-21704600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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