Variant report

Variant	rs9676916
Chromosome Location	chr19:53059235-53059236
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-6	chr19:53058370-53059548	NONHSAT067560

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1676153	0.81[ASN][1000 genomes]
rs2608513	0.86[AMR][1000 genomes]
rs2615587	0.96[CHB][hapmap];0.95[JPT][hapmap]
rs2615588	0.86[AMR][1000 genomes]
rs2617795	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2633513	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2633517	0.82[AMR][1000 genomes]
rs326439	0.88[AMR][1000 genomes]
rs326441	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs326442	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs326444	0.83[ASN][1000 genomes]
rs326446	0.81[ASN][1000 genomes]
rs326449	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs326458	0.82[CHB][hapmap]
rs329967	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs375267	0.81[ASN][1000 genomes]
rs410046	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs422195	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs429367	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs441549	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs445500	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs521703	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs529698	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs607477	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs62117198	0.83[AMR][1000 genomes]
rs62117199	0.85[AMR][1000 genomes]
rs656541	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs666356	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs668882	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs685200	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs781129	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53042000-53070400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:53042200-53068200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:53042600-53061200	ZNF genes & repeats	Liver	Liver
4	chr19:53044800-53061200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:53046200-53059800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:53046400-53069200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:53047400-53068200	ZNF genes & repeats	Thymus	Thymus
8	chr19:53047800-53068600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:53048000-53066400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
10	chr19:53048600-53061200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:53049400-53063800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:53049600-53060400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
13	chr19:53050400-53065400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
14	chr19:53050400-53069200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:53050600-53061200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:53050800-53061200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:53051000-53061400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr19:53051000-53068000	ZNF genes & repeats	Fetal Intestine Large	intestine
19	chr19:53051200-53061200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr19:53051400-53068200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr19:53051600-53059600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:53051600-53061200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:53051600-53061200	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:53051600-53061400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:53051600-53061600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:53051600-53068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:53051600-53068200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
28	chr19:53051600-53073200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:53052000-53067400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr19:53052000-53067800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:53052200-53059600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:53052200-53063400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
33	chr19:53052200-53067800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr19:53053200-53059600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:53053600-53067800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
36	chr19:53054000-53059400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
37	chr19:53054000-53060000	ZNF genes & repeats	Fetal Lung	lung
38	chr19:53054200-53061200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr19:53054200-53061200	ZNF genes & repeats	Left Ventricle	heart
40	chr19:53054600-53061000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr19:53054600-53064200	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr19:53055200-53061200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
43	chr19:53055800-53059800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr19:53055800-53061200	ZNF genes & repeats	HMEC	breast
45	chr19:53056000-53059400	ZNF genes & repeats	HSMMtube	muscle
46	chr19:53056000-53061400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
47	chr19:53056200-53065800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:53056400-53060800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:53056600-53065400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:53056800-53059400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell

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