Variant report

Variant	rs62121392
Chromosome Location	chr19:38537588-38537589
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38392598..38394693-chr19:38535463..38537612,2	MCF-7	breast:
2	chr19:38536919..38539857-chr19:38546336..38549033,2	MCF-7	breast:
3	chr19:38395411..38398481-chr19:38535356..38538945,3	MCF-7	breast:
4	chr19:38525040..38526953-chr19:38535693..38538663,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	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];0.83[ASN][1000 genomes]
rs57844882	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61657018	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62121389	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121390	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121391	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121394	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38538400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:38521800-38538400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr19:38524400-38538400	Weak transcription	Small Intestine	intestine
6	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:38525800-38538000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:38526000-38537600	Weak transcription	Fetal Intestine Large	intestine
9	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
10	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
11	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
13	chr19:38528600-38538200	Weak transcription	HSMMtube	muscle
14	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:38529000-38537800	Weak transcription	Fetal Muscle Leg	muscle
16	chr19:38529000-38538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
18	chr19:38531000-38538400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:38531400-38550800	Weak transcription	NHLF	lung
20	chr19:38531600-38539000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38534200-38539600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:38534400-38538600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
26	chr19:38534600-38538200	Weak transcription	Lung	lung
27	chr19:38534600-38538600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:38534600-38539400	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:38534800-38537800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:38535000-38538000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:38535200-38540000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:38535400-38537800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:38535400-38538200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:38535400-38538200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:38535400-38538800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38535400-38539400	Enhancers	Primary B cells from cord blood	blood
38	chr19:38535600-38537600	Weak transcription	NH-A	brain
39	chr19:38535800-38538000	Weak transcription	Osteobl	bone
40	chr19:38535800-38539200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38536000-38538600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:38536000-38539200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr19:38536000-38539200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
45	chr19:38536200-38537600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
46	chr19:38536200-38538600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr19:38536200-38538600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr19:38536200-38539200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr19:38536200-38539400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:38536200-38539400	Flanking Active TSS	GM12878-XiMat	blood

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