Variant report

Variant	rs1546800
Chromosome Location	chr19:38547506-38547507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38395738..38398220-chr19:38547451..38552123,4	MCF-7	breast:
2	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:
3	chr19:38536919..38539857-chr19:38546336..38549033,2	MCF-7	breast:
4	chr19:38540614..38543298-chr19:38547451..38549328,2	MCF-7	breast:
5	chr19:38547326..38550182-chr19:38558061..38560076,2	MCF-7	breast:
6	chr19:38546251..38550140-chr19:38563809..38566619,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

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

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

rs_ID	r²[population]
rs16979230	0.83[EUR][1000 genomes]
rs57844882	0.90[EUR][1000 genomes]
rs61657018	0.92[EUR][1000 genomes]
rs62121389	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62121390	0.89[EUR][1000 genomes]
rs62121391	0.89[EUR][1000 genomes]
rs62121392	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62121394	0.83[AMR][1000 genomes];0.92[EUR][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	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
3	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
4	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
6	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
7	chr19:38531400-38550800	Weak transcription	NHLF	lung
8	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
10	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
13	chr19:38539200-38548800	Weak transcription	Colonic Mucosa	Colon
14	chr19:38539200-38548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
16	chr19:38540200-38548600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:38540400-38551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:38540600-38548800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:38540600-38549000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:38540800-38548800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:38540800-38549800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:38541000-38548600	Weak transcription	Primary T cells from cord blood	blood
23	chr19:38541400-38548600	Weak transcription	GM12878-XiMat	blood
24	chr19:38543400-38553600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:38543800-38549000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:38544000-38548600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:38544200-38548200	Strong transcription	Fetal Intestine Small	intestine
29	chr19:38545600-38547600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38545800-38548600	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:38545800-38550400	Weak transcription	Spleen	Spleen
32	chr19:38545800-38550800	Weak transcription	Osteobl	bone
33	chr19:38545800-38553600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:38546000-38548600	Weak transcription	Stomach Mucosa	stomach
35	chr19:38546200-38548600	Weak transcription	Thymus	Thymus
36	chr19:38546200-38551800	Weak transcription	HSMMtube	muscle
37	chr19:38546400-38548600	Weak transcription	Primary B cells from cord blood	blood
38	chr19:38546400-38549000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr19:38546400-38550000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr19:38546400-38550000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr19:38546400-38550200	Weak transcription	HUVEC	blood vessel
42	chr19:38546400-38553600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:38546600-38548600	Weak transcription	Brain Angular Gyrus	brain
44	chr19:38546600-38548600	Weak transcription	Fetal Intestine Large	intestine
45	chr19:38546600-38549200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:38546600-38549600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:38546600-38553600	Weak transcription	Brain Substantia Nigra	brain
48	chr19:38546600-38554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:38546800-38548600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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