Variant report

Variant	rs11669033
Chromosome Location	chr19:21596023-21596024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-2	chr19:21594742-21597401	NONHSAT063703

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

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10414834	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424079	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666213	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666540	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11667103	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11667361	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11667392	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11669790	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670815	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11670868	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11672341	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11672583	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11673320	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11879901	0.92[EUR][1000 genomes]
rs13346641	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1621154	0.91[EUR][1000 genomes]
rs1626404	0.91[EUR][1000 genomes]
rs1762578	0.91[EUR][1000 genomes]
rs17680605	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1781867	0.91[EUR][1000 genomes]
rs1781872	0.91[EUR][1000 genomes]
rs1967182	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061916	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2154302	0.89[EUR][1000 genomes]
rs2358993	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2359144	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562405	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562413	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2650776	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650844	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650848	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs279807	0.86[EUR][1000 genomes]
rs279809	0.87[EUR][1000 genomes]
rs2914646	0.84[AFR][1000 genomes]
rs3853837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321312	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4327181	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4359573	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4544364	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4638726	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55756795	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55790393	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55875743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55899865	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs57299552	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58412280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60173523	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61035285	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107465	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62107468	0.82[EUR][1000 genomes]
rs62107469	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107472	0.91[EUR][1000 genomes]
rs62107479	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107531	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107534	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107536	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62107539	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62107540	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62107541	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109226	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62109227	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62109228	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62109229	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110071	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62110367	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62110377	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62110416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110426	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110427	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110428	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110429	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246339	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7251135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258099	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7258473	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7258562	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73537884	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11669033	ZNF708	cis	lung	GTEx
rs11669033	ZNF708	cis	Muscle Skeletal	GTEx
rs11669033	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11669033	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11669033	RP11-678G14.2	cis	Whole Blood	GTEx
rs11669033	RP11-678G14.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21600200	Weak transcription	Gastric	stomach
2	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21581000-21596200	Weak transcription	Aorta	Aorta
4	chr19:21581000-21598800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21581400-21596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:21581400-21598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:21583800-21596200	Weak transcription	Brain Substantia Nigra	brain
10	chr19:21583800-21598200	Weak transcription	Fetal Brain Male	brain
11	chr19:21584000-21596200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:21584000-21596200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:21584000-21597400	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:21584800-21598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:21585000-21596800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:21586000-21599400	Weak transcription	Spleen	Spleen
18	chr19:21586600-21596200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:21586800-21598400	Weak transcription	Colonic Mucosa	Colon
20	chr19:21588200-21598600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:21588400-21596600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:21588400-21597600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:21588600-21596600	Strong transcription	Fetal Stomach	stomach
24	chr19:21588800-21596200	Weak transcription	Fetal Thymus	thymus
25	chr19:21589600-21598200	Weak transcription	NHDF-Ad	bronchial
26	chr19:21590000-21600200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr19:21590600-21598400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:21590600-21598600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:21590800-21601200	Strong transcription	Ovary	ovary
32	chr19:21591200-21597000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:21591600-21599000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr19:21591800-21597200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
36	chr19:21592000-21597600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:21592200-21596800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:21592200-21597200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:21592200-21597600	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr19:21592200-21597800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr19:21592400-21597400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:21592400-21598600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
43	chr19:21592600-21596200	Weak transcription	Right Ventricle	heart
44	chr19:21592600-21598200	Weak transcription	Brain Hippocampus Middle	brain
45	chr19:21592800-21596200	Weak transcription	Brain Anterior Caudate	brain
46	chr19:21592800-21596200	Weak transcription	NH-A	brain
47	chr19:21592800-21601200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:21593200-21602400	Weak transcription	HSMM	muscle
49	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
50	chr19:21593600-21596800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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