Variant report

Variant	rs10414834
Chromosome Location	chr19:21606719-21606720
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-1	chr19:21605958-21608304	ENSG00000196686

Extended variants
information (count: 114 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10410762	1.00[YRI][hapmap]
rs10424079	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666525	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666540	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11667103	0.87[EUR][1000 genomes]
rs11667361	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11667392	0.81[EUR][1000 genomes]
rs11669033	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669790	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670815	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670868	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11672341	0.88[EUR][1000 genomes]
rs11672583	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11879901	0.88[EUR][1000 genomes]
rs13346641	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1566475	1.00[YRI][hapmap]
rs1621154	0.87[EUR][1000 genomes]
rs1626404	0.87[EUR][1000 genomes]
rs1762578	0.87[EUR][1000 genomes]
rs17680605	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1781867	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs1781872	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1967182	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061916	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2154302	0.85[EUR][1000 genomes]
rs2358993	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2359144	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359146	1.00[YRI][hapmap]
rs2562405	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562416	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2562456	0.89[CEU][hapmap]
rs2650755	1.00[YRI][hapmap]
rs2650776	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650793	0.89[CEU][hapmap]
rs2650805	0.94[CEU][hapmap]
rs2650844	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650846	1.00[YRI][hapmap]
rs2650848	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs279807	0.82[EUR][1000 genomes]
rs279809	0.83[EUR][1000 genomes]
rs2914632	1.00[YRI][hapmap]
rs3853837	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853838	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321312	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4327181	0.87[EUR][1000 genomes]
rs4359573	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4544364	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4638726	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808280	1.00[YRI][hapmap]
rs55756795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55790393	0.87[EUR][1000 genomes]
rs55875743	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55899865	0.87[EUR][1000 genomes]
rs57299552	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58412280	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60173523	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61035285	0.88[EUR][1000 genomes]
rs62107465	0.85[EUR][1000 genomes]
rs62107469	0.85[EUR][1000 genomes]
rs62107472	0.87[EUR][1000 genomes]
rs62107479	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107531	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107532	0.88[EUR][1000 genomes]
rs62107534	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107536	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62107539	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107540	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107541	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62109225	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62109226	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109227	0.90[AMR][1000 genomes]
rs62109228	0.90[AMR][1000 genomes]
rs62109229	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110071	0.83[EUR][1000 genomes]
rs62110367	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110377	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110416	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110420	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110424	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110426	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110427	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627522	0.94[CEU][hapmap]
rs6511253	0.94[CEU][hapmap]
rs7246339	0.87[EUR][1000 genomes]
rs7251135	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7254098	1.00[YRI][hapmap]
rs7258099	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258473	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7258562	0.87[EUR][1000 genomes]
rs7260065	0.88[CEU][hapmap]
rs73537884	0.88[EUR][1000 genomes]
rs939300	1.00[YRI][hapmap]

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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10414834	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs10414834	ZNF708	cis	lung	GTEx
rs10414834	ZNF708	cis	Muscle Skeletal	GTEx
rs10414834	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs10414834	ZNF708	cis	Thyroid	GTEx
rs10414834	RP11-678G14.2	cis	Whole Blood	GTEx
rs10414834	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
4	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
5	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
6	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21600200-21606800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:21600200-21608200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:21600800-21607800	ZNF genes & repeats	Dnd41	blood
11	chr19:21601200-21607600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
12	chr19:21602000-21608200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr19:21603400-21609400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:21604200-21607600	ZNF genes & repeats	Fetal Brain Female	brain
15	chr19:21604400-21606800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:21604400-21609200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr19:21604400-21610400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr19:21604600-21608000	ZNF genes & repeats	Fetal Lung	lung
19	chr19:21604600-21608400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr19:21604800-21608800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr19:21605200-21608000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
22	chr19:21605600-21607200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:21605600-21608000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr19:21605600-21610800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:21605600-21610800	Weak transcription	Ovary	ovary
26	chr19:21605800-21607600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
27	chr19:21605800-21609400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
28	chr19:21606000-21606800	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr19:21606000-21606800	ZNF genes & repeats	HSMM	muscle
30	chr19:21606000-21607600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
31	chr19:21606000-21608800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood

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