Variant report

Variant	rs4670952
Chromosome Location	chr2:39893939-39893940
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	chr2:39893666..39896624-chr2:39898263..39900295,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10170462	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177801	0.85[EUR][1000 genomes]
rs10186346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10208929	0.85[EUR][1000 genomes]
rs11124689	0.85[EUR][1000 genomes]
rs12613210	0.87[EUR][1000 genomes]
rs12712652	0.96[EUR][1000 genomes]
rs12989245	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13384364	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13405084	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13409487	0.96[EUR][1000 genomes]
rs1548870	0.85[EUR][1000 genomes]
rs1548871	0.85[EUR][1000 genomes]
rs1861244	0.96[EUR][1000 genomes]
rs2041736	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2058618	0.96[EUR][1000 genomes]
rs2215956	0.85[EUR][1000 genomes]
rs2540200	0.94[EUR][1000 genomes]
rs2540247	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2540248	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2540249	0.93[EUR][1000 genomes]
rs2540250	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2540251	0.93[EUR][1000 genomes]
rs2540252	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2540255	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2716682	0.88[EUR][1000 genomes]
rs2716683	0.87[EUR][1000 genomes]
rs2716684	0.87[EUR][1000 genomes]
rs2716686	0.94[EUR][1000 genomes]
rs2716687	0.94[EUR][1000 genomes]
rs2716688	0.94[EUR][1000 genomes]
rs2716690	0.96[EUR][1000 genomes]
rs2716691	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716692	0.96[EUR][1000 genomes]
rs2716693	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716694	0.87[EUR][1000 genomes]
rs2716719	0.84[EUR][1000 genomes]
rs2716720	0.85[EUR][1000 genomes]
rs2716732	0.96[EUR][1000 genomes]
rs2716737	0.95[EUR][1000 genomes]
rs2716738	0.94[EUR][1000 genomes]
rs35791480	0.86[EUR][1000 genomes]
rs4670954	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6707177	0.83[EUR][1000 genomes]
rs6736442	0.85[EUR][1000 genomes]
rs6748628	0.85[EUR][1000 genomes]
rs917964	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs949812	0.97[EUR][1000 genomes]
rs949813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3411574	chr2:39891873-39894421	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3377107	chr2:39892273-39894821	Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39891200-39894000	Active TSS	Fetal Brain Female	brain
2	chr2:39891800-39894600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:39892000-39894000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:39892000-39894200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:39892000-39894400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:39892200-39894000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr2:39892200-39894000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:39892200-39894000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr2:39892200-39894000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:39892200-39894000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:39892200-39894000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:39892200-39894000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:39892200-39894000	Active TSS	Fetal Kidney	kidney
14	chr2:39892200-39894600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:39892400-39894000	Active TSS	Right Atrium	heart
16	chr2:39892400-39894200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr2:39892400-39894400	Active TSS	Aorta	Aorta
18	chr2:39892600-39894000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39892600-39894200	Bivalent Enhancer	Spleen	Spleen
20	chr2:39892600-39894800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:39892600-39894800	Active TSS	Brain Angular Gyrus	brain
22	chr2:39892800-39894000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr2:39893000-39894000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
24	chr2:39893000-39894000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
25	chr2:39893000-39894200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:39893000-39894200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:39893000-39894200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:39893000-39894200	Flanking Bivalent TSS/Enh	HMEC	breast
29	chr2:39893200-39894000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr2:39893200-39894000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr2:39893200-39894000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
32	chr2:39893200-39894000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:39893200-39894000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
34	chr2:39893200-39894200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:39893200-39894200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:39893200-39894200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:39893200-39894200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr2:39893200-39894200	Flanking Bivalent TSS/Enh	Thymus	Thymus
39	chr2:39893400-39894000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:39893400-39894000	Flanking Active TSS	Lung	lung
41	chr2:39893400-39894200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
42	chr2:39893400-39894200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:39893400-39894400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr2:39893600-39894000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:39893600-39894000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:39893600-39894000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:39893600-39894000	Active TSS	Fetal Brain Male	brain
48	chr2:39893600-39894000	Active TSS	Fetal Heart	heart
49	chr2:39893600-39894000	Flanking Bivalent TSS/Enh	Placenta	Placenta
50	chr2:39893600-39894000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus

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