Variant report

Variant	rs28661145
Chromosome Location	chr19:53588643-53588644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF415-2	chr19:53588371-53588648	NONHSAT067622

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10406237	1.00[ASN][1000 genomes]
rs10409615	1.00[ASN][1000 genomes]
rs10410030	1.00[ASN][1000 genomes]
rs10412805	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10418505	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16984438	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16984443	1.00[ASN][1000 genomes]
rs16984486	1.00[ASN][1000 genomes]
rs28368410	1.00[ASN][1000 genomes]
rs28528321	1.00[ASN][1000 genomes]
rs28662846	1.00[ASN][1000 genomes]
rs28691095	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701520	1.00[ASN][1000 genomes]
rs28726276	1.00[ASN][1000 genomes]
rs58143828	1.00[ASN][1000 genomes]
rs6509721	0.85[EUR][1000 genomes]
rs6509725	1.00[ASN][1000 genomes]
rs7247568	1.00[ASN][1000 genomes]
rs7253566	1.00[ASN][1000 genomes]
rs73935216	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935236	1.00[ASN][1000 genomes]
rs8099848	1.00[ASN][1000 genomes]
rs8100134	1.00[ASN][1000 genomes]
rs8102799	1.00[ASN][1000 genomes]
rs8113824	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers 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	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53570600-53589600	ZNF genes & repeats	GM12878-XiMat	blood
2	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
3	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:53575600-53598600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
7	chr19:53578800-53593400	Weak transcription	HepG2	liver
8	chr19:53580600-53588800	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:53580600-53589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:53580600-53597800	Weak transcription	Fetal Heart	heart
11	chr19:53581000-53591200	Strong transcription	Fetal Intestine Large	intestine
12	chr19:53583800-53589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:53584000-53599000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr19:53584200-53595000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:53584200-53595200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:53584400-53595200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:53584400-53596400	Strong transcription	Fetal Brain Female	brain
18	chr19:53584400-53598000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:53584600-53589600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr19:53584600-53594600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:53584600-53595000	Strong transcription	Brain Cingulate Gyrus	brain
22	chr19:53584600-53599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:53584600-53599800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:53584800-53595400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:53585000-53595200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:53585000-53597000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:53585200-53589600	Strong transcription	Left Ventricle	heart
28	chr19:53585200-53590000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:53585200-53590000	Strong transcription	Brain Hippocampus Middle	brain
30	chr19:53585200-53590600	ZNF genes & repeats	Lung	lung
31	chr19:53585200-53596200	Strong transcription	Thymus	Thymus
32	chr19:53585200-53596400	Strong transcription	Dnd41	blood
33	chr19:53585200-53597800	Strong transcription	Placenta	Placenta
34	chr19:53585200-53599400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:53585200-53599600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr19:53585400-53589600	Strong transcription	A549	lung
37	chr19:53585400-53590000	Strong transcription	Osteobl	bone
38	chr19:53585400-53590600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:53585400-53594400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:53585400-53594400	Strong transcription	Primary B cells from cord blood	blood
41	chr19:53585400-53594400	Strong transcription	Fetal Lung	lung
42	chr19:53585400-53595200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:53585400-53595200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr19:53585400-53604800	Weak transcription	Psoas Muscle	Psoas
45	chr19:53585600-53590200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:53585600-53595200	Strong transcription	Brain Angular Gyrus	brain
47	chr19:53585600-53595200	Strong transcription	Gastric	stomach
48	chr19:53585600-53598800	Strong transcription	HSMMtube	muscle
49	chr19:53585600-53599000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:53585600-53599200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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