Variant report

Variant	rs11706541
Chromosome Location	chr3:52286349-52286350
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52278277..52281486-chr3:52282865..52288389,9	K562	blood:

Variant related genes	Relation type
ENSG00000164088	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10460962	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10461027	0.90[EUR][1000 genomes]
rs10461028	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706515	0.87[EUR][1000 genomes]
rs11707056	0.93[EUR][1000 genomes]
rs11708581	0.87[EUR][1000 genomes]
rs11708811	0.93[EUR][1000 genomes]
rs11710014	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711914	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711974	0.87[EUR][1000 genomes]
rs11713914	0.87[EUR][1000 genomes]
rs11714313	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11714358	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11715208	0.93[EUR][1000 genomes]
rs11715382	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715391	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11717028	0.90[EUR][1000 genomes]
rs11717574	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11718729	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719760	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720365	0.87[EUR][1000 genomes]
rs11721277	0.87[EUR][1000 genomes]
rs17052051	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052052	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17052053	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052054	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1767	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35976326	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733063	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852062	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3886875	0.82[EUR][1000 genomes]
rs4082828	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55676974	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55806905	0.87[EUR][1000 genomes]
rs55813842	0.87[EUR][1000 genomes]
rs55847657	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002041	0.87[EUR][1000 genomes]
rs56322342	0.87[EUR][1000 genomes]
rs56352611	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.87[EUR][1000 genomes]
rs57849650	0.87[EUR][1000 genomes]
rs58531656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61644644	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61729402	1.00[ASN][1000 genomes]
rs61729450	1.00[ASN][1000 genomes]
rs6445385	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6783652	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6793317	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809248	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072990	0.82[EUR][1000 genomes]
rs73088773	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088783	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088785	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088791	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088800	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091166	0.87[EUR][1000 genomes]
rs73091168	0.87[EUR][1000 genomes]
rs746239	0.87[EUR][1000 genomes]
rs7615405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7628461	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7633687	0.87[EUR][1000 genomes]
rs7638204	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643913	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11706541	PPM1M	cis	Nerve Tibial	GTEx
rs11706541	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52279600-52287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52280200-52287600	Weak transcription	HMEC	breast
3	chr3:52280200-52287800	Weak transcription	Small Intestine	intestine
4	chr3:52280200-52290000	Weak transcription	Ovary	ovary
5	chr3:52280400-52287000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:52280400-52291200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:52280600-52287000	Weak transcription	HSMMtube	muscle
8	chr3:52280600-52287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52280600-52288200	Weak transcription	Fetal Kidney	kidney
10	chr3:52280600-52290800	Weak transcription	Psoas Muscle	Psoas
11	chr3:52280600-52292400	Weak transcription	Fetal Heart	heart
12	chr3:52280800-52287400	Weak transcription	K562	blood
13	chr3:52280800-52292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:52281000-52287200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:52281000-52291800	Strong transcription	Fetal Intestine Small	intestine
16	chr3:52281200-52286600	Weak transcription	NHDF-Ad	bronchial
17	chr3:52281200-52287800	Strong transcription	Fetal Stomach	stomach
18	chr3:52281400-52287600	Strong transcription	Fetal Brain Female	brain
19	chr3:52281600-52287000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:52281600-52287200	Genic enhancers	Fetal Thymus	thymus
21	chr3:52281600-52287400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:52281600-52287400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:52281600-52287400	Weak transcription	HepG2	liver
24	chr3:52281800-52286800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:52281800-52287200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:52281800-52287200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:52281800-52287400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52281800-52288200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:52281800-52303400	Weak transcription	Right Atrium	heart
30	chr3:52282000-52286600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:52282000-52286600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:52282000-52287600	Strong transcription	Adipose Nuclei	Adipose
33	chr3:52282000-52298800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:52282000-52299400	Strong transcription	Liver	Liver
35	chr3:52282200-52286800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:52282200-52287000	Strong transcription	Dnd41	blood
37	chr3:52282200-52287400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:52282200-52287600	Strong transcription	Brain Anterior Caudate	brain
39	chr3:52282200-52287600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52282200-52293200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:52282200-52303000	Strong transcription	Fetal Lung	lung
42	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:52282400-52286400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:52282400-52297200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52282600-52286600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:52282600-52286600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:52282600-52286600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:52282600-52289400	Weak transcription	Fetal Brain Male	brain
50	chr3:52282600-52304000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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