Variant report

Variant	rs61644644
Chromosome Location	chr3:52307496-52307497
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	chr3:52306677..52308249-chr3:52309532..52311705,2	MCF-7	breast:
2	chr3:52292200..52293754-chr3:52305089..52307890,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10460962	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.97[EUR][1000 genomes]
rs10461028	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865971	0.83[EUR][1000 genomes]
rs11706515	0.94[EUR][1000 genomes]
rs11706541	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707056	1.00[EUR][1000 genomes]
rs11708581	0.94[EUR][1000 genomes]
rs11708811	1.00[EUR][1000 genomes]
rs11710014	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711974	0.94[EUR][1000 genomes]
rs11713464	0.89[AMR][1000 genomes]
rs11713914	0.94[EUR][1000 genomes]
rs11714313	0.82[AMR][1000 genomes]
rs11714358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715208	1.00[EUR][1000 genomes]
rs11715382	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715391	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11717028	0.97[EUR][1000 genomes]
rs11717574	0.82[AMR][1000 genomes]
rs11718729	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719760	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720365	0.94[EUR][1000 genomes]
rs11721277	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052052	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17052053	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052054	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263770	0.81[EUR][1000 genomes]
rs1767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35976326	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733063	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3852062	0.82[AMR][1000 genomes]
rs3886875	0.88[EUR][1000 genomes]
rs4082828	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55676974	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806905	0.94[EUR][1000 genomes]
rs55813842	0.94[EUR][1000 genomes]
rs55847657	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56002041	0.94[EUR][1000 genomes]
rs56322342	0.94[EUR][1000 genomes]
rs56352611	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56899118	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.94[EUR][1000 genomes]
rs58531656	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58879205	0.89[AMR][1000 genomes]
rs60382084	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445385	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793317	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809248	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724801	0.82[EUR][1000 genomes]
rs729555	0.82[EUR][1000 genomes]
rs73072990	0.88[EUR][1000 genomes]
rs73088773	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088785	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088791	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088800	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091166	0.94[EUR][1000 genomes]
rs73091168	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	0.94[EUR][1000 genomes]
rs7615405	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633687	0.94[EUR][1000 genomes]
rs7638204	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7643913	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61644644	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:52285600-52308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52292400-52309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52293000-52308000	Weak transcription	Stomach Mucosa	stomach
10	chr3:52297400-52311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:52300000-52310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:52300000-52310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52300200-52310200	Weak transcription	HSMMtube	muscle
14	chr3:52300600-52310800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:52301200-52311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:52302600-52307800	Weak transcription	Pancreas	Pancrea
17	chr3:52302600-52310000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52302800-52310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:52303000-52311200	Weak transcription	Esophagus	oesophagus
20	chr3:52303400-52310000	Weak transcription	Aorta	Aorta
21	chr3:52303600-52307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:52303600-52308400	Strong transcription	NHEK	skin
23	chr3:52303600-52309600	Genic enhancers	Primary B cells from cord blood	blood
24	chr3:52303800-52308200	Weak transcription	Gastric	stomach
25	chr3:52303800-52309600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:52304000-52311000	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr3:52304200-52309800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52304400-52310200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:52304800-52308600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
30	chr3:52304800-52309800	Genic enhancers	Dnd41	blood
31	chr3:52305000-52308000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:52305000-52310000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:52305000-52310400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:52305200-52307600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:52305200-52310400	Genic enhancers	Fetal Thymus	thymus
36	chr3:52305600-52309400	Weak transcription	Fetal Kidney	kidney
37	chr3:52305600-52310000	Genic enhancers	HepG2	liver
38	chr3:52305800-52308000	Weak transcription	Fetal Brain Female	brain
39	chr3:52305800-52310200	Genic enhancers	Fetal Muscle Leg	muscle
40	chr3:52305800-52310200	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:52306000-52307600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:52306000-52307600	Strong transcription	Fetal Intestine Small	intestine
43	chr3:52306000-52307800	Weak transcription	Right Atrium	heart
44	chr3:52306000-52308000	Weak transcription	Brain Anterior Caudate	brain
45	chr3:52306000-52308200	Strong transcription	Fetal Stomach	stomach
46	chr3:52306000-52309400	Weak transcription	Brain Angular Gyrus	brain
47	chr3:52306000-52310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:52306200-52307600	Genic enhancers	Placenta	Placenta
49	chr3:52306200-52308400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52306200-52308400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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