Variant report

Variant	rs324093
Chromosome Location	chr19:52956905-52956906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF534-1	chr19:52956835-52962089	NONHSAT067555
2	lnc-ZNF534-1	chr19:52956866-52956970	NONHSAT067557

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1112889	0.87[AFR][1000 genomes]
rs1115659	0.88[AFR][1000 genomes]
rs1115660	0.87[AFR][1000 genomes]
rs12459176	0.89[AFR][1000 genomes]
rs12460429	0.89[AFR][1000 genomes]
rs1428177	0.88[AFR][1000 genomes]
rs1457854	0.89[AFR][1000 genomes]
rs1457855	0.89[AFR][1000 genomes]
rs1457856	0.89[AFR][1000 genomes]
rs1457857	0.85[AFR][1000 genomes]
rs1599602	1.00[EUR][1000 genomes]
rs1817266	0.86[AFR][1000 genomes]
rs1840997	0.88[AFR][1000 genomes]
rs1840998	0.88[AFR][1000 genomes]
rs1864019	0.88[AFR][1000 genomes]
rs2115101	0.89[AFR][1000 genomes]
rs2168792	0.89[AFR][1000 genomes]
rs2903895	0.86[AFR][1000 genomes]
rs324094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324097	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324102	0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324105	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs326450	1.00[EUR][1000 genomes]
rs35170850	0.88[AFR][1000 genomes]
rs4802949	0.88[AFR][1000 genomes]
rs4802950	0.84[AFR][1000 genomes]
rs59465772	1.00[EUR][1000 genomes]
rs60186879	1.00[EUR][1000 genomes]
rs60952057	1.00[EUR][1000 genomes]
rs61039331	1.00[EUR][1000 genomes]
rs6509641	0.86[AFR][1000 genomes]
rs6509643	0.90[AFR][1000 genomes]
rs7252655	0.88[AFR][1000 genomes]
rs8101762	1.00[EUR][1000 genomes]
rs8110920	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3415774	chr19:52938189-52970794	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52954000-52961600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr19:52954400-52961400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:52954400-52962600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:52955600-52957800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
5	chr19:52955800-52957800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
6	chr19:52955800-52958200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
7	chr19:52955800-52961400	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr19:52956000-52957000	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr19:52956000-52957200	Active TSS	Brain Anterior Caudate	brain
10	chr19:52956000-52957600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:52956000-52958000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:52956000-52969600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:52956000-52986200	ZNF genes & repeats	Liver	Liver
14	chr19:52956200-52957000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:52956200-52957000	Active TSS	Brain Angular Gyrus	brain
16	chr19:52956200-52957200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:52956200-52957200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:52956200-52957200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr19:52956200-52957200	Bivalent/Poised TSS	Fetal Brain Female	brain
20	chr19:52956200-52957200	Active TSS	Fetal Heart	heart
21	chr19:52956200-52957200	Active TSS	Right Ventricle	heart
22	chr19:52956200-52957400	Active TSS	Fetal Brain Male	brain
23	chr19:52956200-52957600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:52956200-52957600	Active TSS	Fetal Kidney	kidney
25	chr19:52956200-52957600	ZNF genes & repeats	NHEK	skin
26	chr19:52956200-52957800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:52956200-52958000	Active TSS	NHDF-Ad	bronchial
28	chr19:52956200-52958200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
29	chr19:52956200-52958400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:52956200-52958400	Active TSS	Psoas Muscle	Psoas
31	chr19:52956200-52961400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
32	chr19:52956200-52961400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:52956200-52961600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:52956200-52962800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr19:52956400-52957000	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr19:52956400-52957000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:52956400-52957000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:52956400-52957000	Active TSS	Brain Substantia Nigra	brain
39	chr19:52956400-52957000	Active TSS	Fetal Muscle Trunk	muscle
40	chr19:52956400-52957000	Active TSS	Left Ventricle	heart
41	chr19:52956400-52957000	Active TSS	Pancreas	Pancrea
42	chr19:52956400-52957000	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr19:52956400-52957000	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr19:52956400-52957200	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr19:52956400-52957200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr19:52956400-52957200	Active TSS	Colon Smooth Muscle	Colon
47	chr19:52956400-52957200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:52956400-52957200	Active TSS	Ovary	ovary
49	chr19:52956400-52957200	Active TSS	Right Atrium	heart
50	chr19:52956400-52957200	Active TSS	HSMM	muscle

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