Variant report

Variant	rs11672583
Chromosome Location	chr19:21562165-21562166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-1	chr19:21560191-21571384	NR_027130
2	lnc-ZNF708-8	chr19:21562076-21562253	ucscGeneNc_uc002nqg_2

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10414834	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10424079	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11666213	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11666525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11666540	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11667103	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667361	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11667392	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669033	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11669790	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670815	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11670868	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11673320	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13346641	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1621154	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626404	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762578	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781867	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781872	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967182	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2061916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154302	0.91[EUR][1000 genomes]
rs2358993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359144	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2562405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2562416	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2650776	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2650844	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650848	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs279807	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279809	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914646	0.84[AFR][1000 genomes]
rs3853837	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3853838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4321312	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4327181	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4359573	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638726	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55756795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55875743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55899865	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57299552	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58412280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60173523	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61035285	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62107465	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107468	0.82[EUR][1000 genomes]
rs62107469	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107472	0.92[EUR][1000 genomes]
rs62107479	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107531	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62107534	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107536	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107540	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109226	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62109227	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109228	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109229	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62110071	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110367	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110377	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62110420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62110424	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62110426	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62110427	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62110428	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62110429	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7246339	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258099	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7258473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258562	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7260065	1.00[JPT][hapmap]
rs73537884	0.83[AMR][1000 genomes];0.94[EUR][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	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
14	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
15	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11672583	ZNF708	cis	lung	GTEx
rs11672583	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11672583	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs11672583	RP11-678G14.2	cis	Whole Blood	GTEx
rs11672583	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11672583	ZNF708	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21542400-21562200	Weak transcription	Colon Smooth Muscle	Colon
2	chr19:21542400-21562200	Weak transcription	Fetal Heart	heart
3	chr19:21542400-21563200	Weak transcription	Brain Substantia Nigra	brain
4	chr19:21543000-21563000	Weak transcription	NHLF	lung
5	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:21543600-21563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
16	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:21550800-21562200	Weak transcription	Brain Angular Gyrus	brain
18	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:21552000-21563200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
20	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr19:21554800-21562800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:21555000-21566800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr19:21555800-21567000	ZNF genes & repeats	Dnd41	blood
24	chr19:21556000-21562200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:21556200-21562200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:21556200-21562800	Weak transcription	Brain Anterior Caudate	brain
27	chr19:21556200-21563200	Strong transcription	HSMM	muscle
28	chr19:21556400-21563200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
29	chr19:21556600-21563000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:21556800-21564200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr19:21556800-21569400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr19:21557000-21564600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:21557400-21562600	Strong transcription	Osteobl	bone
34	chr19:21557800-21562200	Weak transcription	HMEC	breast
35	chr19:21557800-21562400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:21558000-21562200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:21558000-21562600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:21558000-21563200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:21558000-21565400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr19:21558000-21566800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
41	chr19:21558000-21567400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr19:21558000-21567400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:21558200-21562600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:21558600-21562600	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr19:21558800-21563000	Strong transcription	Fetal Kidney	kidney
46	chr19:21559000-21562200	Weak transcription	NH-A	brain
47	chr19:21559000-21562600	ZNF genes & repeats	Adipose Nuclei	Adipose
48	chr19:21559000-21563400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:21559000-21563600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:21559000-21564200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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