Variant report

Variant	rs62121389
Chromosome Location	chr19:38534193-38534194
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	chr19:38531805..38534474-chr19:38544324..38547060,2	MCF-7	breast:
2	chr19:38529387..38531297-chr19:38534097..38536082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221258	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1546800	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16979230	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57844882	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61657018	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62121390	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121391	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121392	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121394	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv911656	chr19:38505037-38539988	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38508600-38537000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38514800-38537000	Weak transcription	Colonic Mucosa	Colon
3	chr19:38516800-38536200	Weak transcription	Spleen	Spleen
4	chr19:38517000-38537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:38521800-38537000	Weak transcription	Esophagus	oesophagus
6	chr19:38521800-38538400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:38521800-38538400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:38522000-38536600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:38522200-38537200	Weak transcription	Thymus	Thymus
12	chr19:38524400-38538400	Weak transcription	Small Intestine	intestine
13	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr19:38525200-38536400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:38525200-38536600	Weak transcription	Gastric	stomach
16	chr19:38525800-38537000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:38525800-38538000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr19:38526000-38537600	Weak transcription	Fetal Intestine Large	intestine
19	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
20	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
21	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
23	chr19:38528600-38534200	Weak transcription	NH-A	brain
24	chr19:38528600-38538200	Weak transcription	HSMMtube	muscle
25	chr19:38528800-38534200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:38528800-38534200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:38528800-38534200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:38528800-38534200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:38528800-38534200	Weak transcription	Primary B cells from cord blood	blood
30	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:38529000-38534200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:38529000-38534200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:38529000-38534400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:38529000-38534400	Weak transcription	Lung	lung
35	chr19:38529000-38534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:38529000-38536000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr19:38529000-38537800	Weak transcription	Fetal Muscle Leg	muscle
38	chr19:38529000-38538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
40	chr19:38529200-38534200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:38529400-38534200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:38531000-38534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:38531000-38538400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:38531400-38534200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr19:38531400-38534400	Weak transcription	Osteobl	bone
46	chr19:38531400-38537200	Weak transcription	HSMM	muscle
47	chr19:38531400-38550800	Weak transcription	NHLF	lung
48	chr19:38531600-38535000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:38531600-38539000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:38533000-38534200	Weak transcription	GM12878-XiMat	blood

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