Variant report

Variant	rs60238878
Chromosome Location	chr19:53049654-53049655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10411461	1.00[EUR][1000 genomes]
rs11882836	1.00[EUR][1000 genomes]
rs2162932	1.00[EUR][1000 genomes]
rs2447422	1.00[EUR][1000 genomes]
rs2931759	1.00[EUR][1000 genomes]
rs2931760	1.00[EUR][1000 genomes]
rs55753173	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57548816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58325433	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59230195	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60194947	1.00[EUR][1000 genomes]
rs60404252	1.00[EUR][1000 genomes]
rs60856351	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73576268	1.00[EUR][1000 genomes]
rs73576294	1.00[EUR][1000 genomes]
rs73578242	1.00[EUR][1000 genomes]
rs73584860	1.00[EUR][1000 genomes]
rs73584871	1.00[EUR][1000 genomes]
rs73584874	1.00[EUR][1000 genomes]
rs73586713	1.00[EUR][1000 genomes]
rs73934550	1.00[EUR][1000 genomes]
rs73934555	1.00[EUR][1000 genomes]
rs8109739	1.00[EUR][1000 genomes]
rs8110537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
2	chr19:53032600-53049800	Weak transcription	HepG2	liver
3	chr19:53037600-53051800	Weak transcription	K562	blood
4	chr19:53039000-53052200	Weak transcription	Fetal Brain Male	brain
5	chr19:53039200-53056000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
6	chr19:53039600-53052000	Weak transcription	HSMMtube	muscle
7	chr19:53039800-53050600	Weak transcription	Fetal Lung	lung
8	chr19:53039800-53051600	Weak transcription	Brain Substantia Nigra	brain
9	chr19:53039800-53051600	Weak transcription	Fetal Kidney	kidney
10	chr19:53040000-53051600	Weak transcription	Brain Angular Gyrus	brain
11	chr19:53040000-53051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:53040000-53052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:53040000-53052200	Weak transcription	Psoas Muscle	Psoas
14	chr19:53040000-53054400	Weak transcription	Fetal Heart	heart
15	chr19:53040200-53050000	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:53040200-53051800	Weak transcription	NHDF-Ad	bronchial
17	chr19:53040200-53057400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:53040400-53057600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:53040600-53049800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:53042000-53070400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:53042200-53051600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:53042200-53068200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr19:53042400-53051600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:53042600-53061200	ZNF genes & repeats	Liver	Liver
25	chr19:53043600-53051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:53044000-53056000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr19:53044400-53052200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:53044400-53059000	ZNF genes & repeats	GM12878-XiMat	blood
29	chr19:53044600-53051800	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:53044600-53053200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:53044600-53056000	ZNF genes & repeats	Lung	lung
32	chr19:53044600-53056400	Strong transcription	Dnd41	blood
33	chr19:53044800-53061200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:53045000-53051200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:53045000-53051600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:53045000-53053800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:53045000-53055800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:53045200-53051600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr19:53046000-53052400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr19:53046200-53049800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:53046200-53050200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:53046200-53050400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:53046200-53051600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:53046200-53052000	Strong transcription	Fetal Thymus	thymus
45	chr19:53046200-53055400	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr19:53046200-53056800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr19:53046200-53059800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:53046400-53049800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:53046400-53050400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:53046400-53051600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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