Variant report

Variant	rs11721277
Chromosome Location	chr3:52420901-52420902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
2	chr3:52420073..52422449-chr3:52434521..52436360,2	K562	blood:
3	chr3:52323111..52325556-chr3:52420130..52421774,2	K562	blood:
4	chr3:52420539..52424070-chr3:52425084..52430819,9	K562	blood:
5	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
6	chr3:52280316..52283002-chr3:52418190..52421140,2	K562	blood:
7	chr3:52312722..52314589-chr3:52419579..52422419,2	MCF-7	breast:
8	chr3:52419090..52421222-chr3:52428572..52431039,2	MCF-7	breast:
9	chr3:52250996..52253546-chr3:52419538..52422445,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239557	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10460962	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865971	0.88[EUR][1000 genomes]
rs11706515	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706541	0.87[EUR][1000 genomes]
rs11707056	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11707864	0.81[AFR][1000 genomes]
rs11708581	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708811	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709658	0.85[AFR][1000 genomes]
rs11710014	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11711974	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713914	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714358	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714402	0.81[AFR][1000 genomes]
rs11715208	0.94[EUR][1000 genomes]
rs11715382	0.86[EUR][1000 genomes]
rs11715391	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11716017	0.81[AFR][1000 genomes]
rs11716487	0.83[EUR][1000 genomes]
rs11717028	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.90[EUR][1000 genomes]
rs11719760	0.87[EUR][1000 genomes]
rs11720365	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs123602	0.80[AFR][1000 genomes]
rs13075370	0.86[AFR][1000 genomes]
rs13076890	0.83[AFR][1000 genomes]
rs17052051	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17052052	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052053	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17052054	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17263770	0.87[EUR][1000 genomes]
rs1767	0.90[EUR][1000 genomes]
rs1769	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34355561	0.81[AFR][1000 genomes]
rs34908451	0.81[AFR][1000 genomes]
rs35976326	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3733063	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3752819	0.83[AFR][1000 genomes]
rs3886875	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4082828	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55676974	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55806905	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55813842	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55847657	0.90[EUR][1000 genomes]
rs56002041	1.00[EUR][1000 genomes]
rs56322342	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352611	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56899118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57849650	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58531656	0.90[EUR][1000 genomes]
rs60382084	0.90[EUR][1000 genomes]
rs61644644	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6445385	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67248391	0.84[AFR][1000 genomes]
rs6776759	0.87[EUR][1000 genomes]
rs67834575	0.84[AFR][1000 genomes]
rs6783652	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6793317	0.90[EUR][1000 genomes]
rs6809248	0.90[EUR][1000 genomes]
rs724801	0.88[EUR][1000 genomes]
rs729555	0.88[EUR][1000 genomes]
rs73072990	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088773	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088783	0.90[EUR][1000 genomes]
rs73088785	0.90[EUR][1000 genomes]
rs73088791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088800	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73091166	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs746239	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615405	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7633687	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638204	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7643913	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11721277	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
3	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
5	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
6	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
8	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
10	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
17	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:52409800-52425200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52410000-52425200	Weak transcription	Primary B cells from cord blood	blood
20	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:52410200-52425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:52410200-52426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:52410600-52422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:52410600-52424800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:52410600-52425000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:52411000-52425200	Weak transcription	Pancreas	Pancrea
29	chr3:52411400-52422200	Weak transcription	Placenta	Placenta
30	chr3:52411400-52424800	Weak transcription	Gastric	stomach
31	chr3:52413800-52433000	Weak transcription	Fetal Brain Female	brain
32	chr3:52414000-52433200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
34	chr3:52414200-52421400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:52414200-52425000	Weak transcription	Right Ventricle	heart
36	chr3:52414600-52421000	Weak transcription	Ovary	ovary
37	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:52416600-52425200	Weak transcription	Esophagus	oesophagus
39	chr3:52418600-52421600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
41	chr3:52418800-52421200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:52418800-52422200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:52418800-52422200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:52418800-52430000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:52418800-52430000	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:52418800-52430600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
48	chr3:52419000-52423600	Strong transcription	Adipose Nuclei	Adipose
49	chr3:52419000-52425200	Strong transcription	Spleen	Spleen
50	chr3:52419000-52431200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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