Variant report

Variant	rs16987292
Chromosome Location	chr19:57005552-57005553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:57002795..57005630-chr19:57006374..57008169,2	MCF-7	breast:

(count:10 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC004696.1-1	chr19:57005532-57006805	NONHSAT068156
2	lnc-AC004696.1-1	chr19:57005532-57005711	ENSG00000166770.6
3	lnc-AC004696.1-1	chr19:57005532-57005711	ENSG00000166770.6
4	lnc-AC004696.1-1	chr19:57005532-57005711	ENSG00000166770.6
5	lnc-AC004696.1-1	chr19:57005532-57005688	ENSG00000166770.6
6	lnc-AC004696.1-1	chr19:57005532-57005972	ENSG00000166770.6
7	lnc-AC004696.1-1	chr19:57005532-57005676	ENSG00000166770.6
8	lnc-AC004696.1-1	chr19:57005532-57005696	ENSG00000166770.6
9	lnc-AC004696.1-1	chr19:57005532-57006801	ENSG00000166770.6
10	lnc-AC004696.1-1	chr19:57005532-57006805	NONHSAT068157

No data

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10415229	0.83[AMR][1000 genomes]
rs10416247	0.84[AFR][1000 genomes]
rs16987287	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56990800-57010000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:56991200-57006800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr19:56991200-57006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56992000-57009400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr19:56992000-57009800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56998600-57008800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:56999800-57006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:57001000-57005600	Weak transcription	HSMM	muscle
9	chr19:57001800-57005800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr19:57002200-57005600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:57002800-57006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:57003000-57018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:57003200-57018400	Weak transcription	Osteobl	bone
14	chr19:57003600-57006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:57003600-57017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:57003800-57005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:57003800-57006800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:57003800-57011600	Weak transcription	Fetal Heart	heart
19	chr19:57004400-57005600	ZNF genes & repeats	Psoas Muscle	Psoas
20	chr19:57004400-57006800	Weak transcription	Fetal Brain Male	brain
21	chr19:57004400-57008800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:57004600-57005800	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr19:57004600-57009400	ZNF genes & repeats	Ovary	ovary
24	chr19:57004600-57009600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:57004800-57005800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
26	chr19:57004800-57006400	ZNF genes & repeats	Fetal Kidney	kidney
27	chr19:57004800-57007800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:57004800-57007800	Strong transcription	Right Ventricle	heart
29	chr19:57005000-57006600	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:57005000-57006800	Weak transcription	Fetal Intestine Large	intestine
31	chr19:57005000-57007000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:57005200-57005800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:57005200-57005800	ZNF genes & repeats	Fetal Stomach	stomach
34	chr19:57005200-57006000	ZNF genes & repeats	Brain Substantia Nigra	brain
35	chr19:57005200-57006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:57005200-57008000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:57005400-57005600	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr19:57005400-57005600	ZNF genes & repeats	Brain Hippocampus Middle	brain
39	chr19:57005400-57005600	ZNF genes & repeats	Pancreas	Pancrea
40	chr19:57005400-57005600	ZNF genes & repeats	HSMMtube	muscle
41	chr19:57005400-57005800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:57005400-57005800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:57005400-57005800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:57005400-57005800	ZNF genes & repeats	Brain Angular Gyrus	brain
45	chr19:57005400-57005800	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:57005400-57005800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:57005400-57005800	ZNF genes & repeats	Gastric	stomach
48	chr19:57005400-57005800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
49	chr19:57005400-57006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:57005400-57006800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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