Variant report

Variant	rs56899118
Chromosome Location	chr3:52397419-52397420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52393007..52395595-chr3:52397371..52399366,2	K562	blood:
2	chr3:52388262..52390856-chr3:52397247..52399479,2	K562	blood:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

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	0.85[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	0.89[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	0.93[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	0.84[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	0.85[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]
rs11721277	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13075370	0.90[AFR][1000 genomes]
rs13076890	0.86[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	0.85[AFR][1000 genomes]
rs34908451	0.85[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	0.87[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	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352611	0.83[AMR][1000 genomes];0.90[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	0.88[AFR][1000 genomes]
rs6776759	0.87[EUR][1000 genomes]
rs67834575	0.88[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	1.00[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	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
2	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
3	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
4	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
5	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56899118	PPM1M	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
2	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
3	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:52375400-52405600	Strong transcription	Lung	lung
5	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:52377000-52406600	Strong transcription	Liver	Liver
8	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
15	chr3:52378400-52400000	Strong transcription	Brain Anterior Caudate	brain
16	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:52378400-52401200	Strong transcription	Gastric	stomach
18	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:52378600-52400000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:52378600-52400200	Strong transcription	Brain Cingulate Gyrus	brain
21	chr3:52378600-52400200	Strong transcription	Brain Hippocampus Middle	brain
22	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:52380400-52401000	Strong transcription	Placenta	Placenta
26	chr3:52381400-52401200	Strong transcription	Ovary	ovary
27	chr3:52381400-52402600	Strong transcription	Fetal Stomach	stomach
28	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:52381400-52407400	Weak transcription	NHLF	lung
30	chr3:52381600-52397600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
32	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:52383000-52401400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52384600-52406200	Weak transcription	GM12878-XiMat	blood
35	chr3:52385400-52398400	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
37	chr3:52386000-52406600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:52387400-52400600	Weak transcription	Dnd41	blood
39	chr3:52387600-52402200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:52388600-52403400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:52390400-52403200	Strong transcription	Spleen	Spleen
42	chr3:52390400-52405600	Weak transcription	Fetal Brain Female	brain
43	chr3:52391400-52400000	Strong transcription	Brain Angular Gyrus	brain
44	chr3:52391400-52401000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:52391600-52398600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:52391600-52399600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:52391600-52399600	Strong transcription	Pancreas	Pancrea
48	chr3:52391600-52399600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:52391600-52401400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:52391800-52397600	Strong transcription	Right Ventricle	heart

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