Variant report

Variant	rs12972550
Chromosome Location	chr19:44843713-44843714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44832482..44835383-chr19:44840174..44844169,3	MCF-7	breast:
2	chr19:44841442..44843915-chr19:44859282..44861440,2	MCF-7	breast:
3	chr19:44840012..44842382-chr19:44842784..44845287,2	MCF-7	breast:
4	chr19:44807123..44810005-chr19:44842666..44844812,2	MCF-7	breast:
5	chr19:44833757..44836676-chr19:44841493..44843748,2	K562	blood:

Variant related genes	Relation type
ENSG00000062370	Chromatin interaction
ENSG00000159917	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011567	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670157	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671074	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12151072	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460431	0.81[AMR][1000 genomes]
rs12981298	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1434575	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1434576	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897826	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014501	0.89[ASN][1000 genomes]
rs2051058	0.83[AMR][1000 genomes]
rs2196184	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2196186	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2196187	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356881	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592768	0.82[AMR][1000 genomes]
rs4802217	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4803697	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67711424	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251134	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252577	0.88[ASN][1000 genomes]
rs7256402	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs733265	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7508523	0.83[AMR][1000 genomes]
rs8104642	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109706	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9676368	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs984117	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912110	chr19:44840789-44902190	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44823200-44856200	ZNF genes & repeats	Liver	Liver
2	chr19:44825000-44846600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:44828000-44845000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr19:44828400-44846400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr19:44828600-44844200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:44828600-44845600	ZNF genes & repeats	Fetal Lung	lung
7	chr19:44828600-44848800	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:44828600-44851000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:44828800-44846200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:44828800-44846400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44829000-44844000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:44830400-44845000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr19:44830600-44845200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr19:44830800-44845600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:44830800-44850400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:44831600-44846600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:44831800-44845000	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr19:44831800-44846400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:44832000-44845600	Weak transcription	Hela-S3	cervix
20	chr19:44832000-44848200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:44837400-44844800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr19:44837400-44845200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
23	chr19:44837400-44851000	ZNF genes & repeats	Ovary	ovary
24	chr19:44839400-44845000	Strong transcription	NH-A	brain
25	chr19:44839400-44845200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:44839400-44845600	Weak transcription	Stomach Mucosa	stomach
27	chr19:44839800-44846400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:44840000-44845400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:44840400-44845200	Strong transcription	HSMM	muscle
30	chr19:44840400-44846200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:44840600-44844600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:44840800-44844200	Strong transcription	Osteobl	bone
33	chr19:44840800-44845400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr19:44840800-44846200	Strong transcription	Brain Angular Gyrus	brain
35	chr19:44840800-44860000	Weak transcription	NHDF-Ad	bronchial
36	chr19:44841000-44847400	Weak transcription	Primary B cells from cord blood	blood
37	chr19:44841200-44844400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:44841200-44844600	Weak transcription	Primary T cells from cord blood	blood
39	chr19:44841200-44846400	Weak transcription	NHLF	lung
40	chr19:44841200-44847000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:44841800-44844600	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:44841800-44846600	ZNF genes & repeats	Adipose Nuclei	Adipose
43	chr19:44842000-44844600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:44842200-44844200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr19:44842200-44845000	Strong transcription	Brain Anterior Caudate	brain
46	chr19:44842200-44845000	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr19:44842200-44845200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:44842200-44846200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr19:44842200-44846200	ZNF genes & repeats	Aorta	Aorta
50	chr19:44842400-44844000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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