Variant report

Variant	rs62117246
Chromosome Location	chr19:53085393-53085394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53073084..53075502-chr19:53084084..53086911,2	K562	blood:

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs368683	0.89[EUR][1000 genomes]
rs369009	0.89[EUR][1000 genomes]
rs374395	0.89[EUR][1000 genomes]
rs45586042	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544769	0.89[EUR][1000 genomes]
rs62117248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62117249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650750	0.89[EUR][1000 genomes]
rs661876	0.89[EUR][1000 genomes]
rs8105873	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074200-53087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:53074400-53085800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr19:53074600-53085800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:53074600-53087400	Weak transcription	Fetal Heart	heart
5	chr19:53074600-53088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
7	chr19:53075400-53089600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:53075400-53092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:53075400-53092400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:53075400-53092400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:53075600-53085600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:53075600-53087000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:53075600-53087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:53075800-53085600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:53075800-53085600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:53075800-53087400	Strong transcription	Osteobl	bone
17	chr19:53075800-53088000	Strong transcription	Rectal Smooth Muscle	rectum
18	chr19:53076400-53096000	Strong transcription	Dnd41	blood
19	chr19:53077600-53088000	Strong transcription	Fetal Brain Female	brain
20	chr19:53079200-53086400	Strong transcription	Ovary	ovary
21	chr19:53079200-53087400	Strong transcription	Brain Anterior Caudate	brain
22	chr19:53079200-53087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:53079200-53092200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:53079400-53087000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:53079400-53087400	Strong transcription	Brain Germinal Matrix	brain
26	chr19:53079400-53087600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr19:53079400-53087600	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:53079400-53088000	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr19:53079400-53089400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr19:53079400-53090400	ZNF genes & repeats	Liver	Liver
31	chr19:53079400-53092200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
32	chr19:53079400-53094200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:53079400-53096000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr19:53079600-53089600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:53079600-53091800	ZNF genes & repeats	Thymus	Thymus
36	chr19:53079800-53089200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:53079800-53091000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:53080200-53085400	Weak transcription	Stomach Mucosa	stomach
39	chr19:53080200-53089400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:53080600-53085400	Weak transcription	Psoas Muscle	Psoas
41	chr19:53081200-53086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr19:53081600-53087000	Strong transcription	HSMM	muscle
43	chr19:53081600-53087200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr19:53081600-53088400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:53081600-53090200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr19:53082000-53085400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:53082000-53085800	ZNF genes & repeats	Esophagus	oesophagus
48	chr19:53082200-53089200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
49	chr19:53082400-53087000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:53082600-53086000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood

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