Variant report

Variant	rs11670607
Chromosome Location	chr19:52898959-52898960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-1	chr19:52897584-52899003	ENSG00000246015
2	lnc-ZNF83-1	chr19:52898851-52899003	ENSG00000269834.1
3	lnc-ZNF83-1	chr19:52897580-52899003	NONHSAT067544
4	lnc-ZNF83-1	chr19:52897580-52899003	NONHSAT067545
5	lnc-ZNF83-1	chr19:52897580-52899003	NONHSAT067546
6	lnc-ZNF83-1	chr19:52898780-52899003	ENSG00000269834.1

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10406795	0.82[CEU][hapmap]
rs11084158	0.80[EUR][1000 genomes]
rs11666879	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11672854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836094	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2290747	0.82[CEU][hapmap]
rs2560993	0.86[EUR][1000 genomes]
rs56778898	0.87[EUR][1000 genomes]
rs60807333	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic 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	16 gene(s)	inside rSNPs	diseases
5	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11670607	ZNF534	cis	lung	GTEx
rs11670607	ZNF534	cis	Nerve Tibial	GTEx
rs11670607	ZNF534	cis	Artery Tibial	GTEx
rs11670607	ZNF534	cis	Adipose Subcutaneous	GTEx
rs11670607	ZNF534	cis	Skin Sun Exposed Lower leg	GTEx
rs11670607	ZNF534	cis	Thyroid	GTEx
rs11670607	ZNF528	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
3	chr19:52891600-52899800	ZNF genes & repeats	Fetal Brain Female	brain
4	chr19:52893400-52900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:52893800-52899600	Weak transcription	Right Ventricle	heart
6	chr19:52894000-52900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:52895600-52900400	ZNF genes & repeats	Fetal Stomach	stomach
8	chr19:52896400-52900200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52896600-52900400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:52896800-52899200	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:52896800-52900200	ZNF genes & repeats	Fetal Lung	lung
12	chr19:52896800-52900400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:52896800-52900600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:52897200-52900400	ZNF genes & repeats	Fetal Muscle Leg	muscle
15	chr19:52897400-52899200	ZNF genes & repeats	Aorta	Aorta
16	chr19:52897400-52899600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:52897400-52899600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:52897400-52899800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:52897400-52899800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:52897400-52900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:52897400-52900000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:52897400-52900000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:52897400-52900200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
24	chr19:52897400-52900200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
25	chr19:52897400-52900200	ZNF genes & repeats	Ovary	ovary
26	chr19:52897400-52900400	ZNF genes & repeats	Liver	Liver
27	chr19:52897400-52900400	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:52897400-52900600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:52897600-52899000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:52897600-52899000	Strong transcription	Brain Hippocampus Middle	brain
31	chr19:52897600-52899200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr19:52897600-52899200	ZNF genes & repeats	Fetal Brain Male	brain
33	chr19:52897600-52899800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:52897600-52900000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:52897600-52900200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:52897600-52900200	ZNF genes & repeats	Fetal Kidney	kidney
37	chr19:52897600-52900200	ZNF genes & repeats	Spleen	Spleen
38	chr19:52897600-52900400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:52897600-52900400	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr19:52897600-52900400	ZNF genes & repeats	Lung	lung
41	chr19:52897600-52901000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:52897800-52899200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:52897800-52899600	Strong transcription	Left Ventricle	heart
44	chr19:52897800-52899600	Strong transcription	Osteobl	bone
45	chr19:52897800-52900000	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:52897800-52900000	Weak transcription	Psoas Muscle	Psoas
47	chr19:52898000-52899400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:52898000-52899600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:52898000-52900200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr19:52898000-52900200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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