Variant report

Variant	rs62246402
Chromosome Location	chr3:47088668-47088669
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:47088626-47088856	K562	blood:	n/a	chr3:47088714-47088725
2	POLR2A	chr3:47088654-47088756	ProgFib	skin:	n/a	n/a
3	CEBPB	chr3:47088631-47088824	HepG2	liver:	n/a	chr3:47088714-47088725

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47081998..47084579-chr3:47088555..47090930,2	K562	blood:

Variant related genes	Relation type
SETD2	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11709660	0.81[AFR][1000 genomes]
rs11713693	0.81[AFR][1000 genomes]
rs11715121	0.81[AFR][1000 genomes]
rs11917361	0.81[AFR][1000 genomes]
rs12493425	0.81[AFR][1000 genomes]
rs12715421	0.85[AFR][1000 genomes]
rs17784031	0.84[EUR][1000 genomes]
rs1982510	0.88[EUR][1000 genomes]
rs4018905	0.82[AFR][1000 genomes]
rs4683322	0.81[AFR][1000 genomes]
rs55691981	0.81[EUR][1000 genomes]
rs55786350	0.81[EUR][1000 genomes]
rs57756484	0.81[AFR][1000 genomes]
rs62246361	0.83[EUR][1000 genomes]
rs62246379	0.84[EUR][1000 genomes]
rs62246398	0.81[AFR][1000 genomes]
rs62246404	0.94[EUR][1000 genomes]
rs62246409	0.91[EUR][1000 genomes]
rs62246455	0.81[AFR][1000 genomes]
rs6414435	0.87[AFR][1000 genomes]
rs6414436	0.82[AFR][1000 genomes]
rs6442055	0.85[AFR][1000 genomes]
rs6442059	0.81[AFR][1000 genomes]
rs6767218	0.81[AFR][1000 genomes]
rs6767907	0.81[AFR][1000 genomes]
rs6768722	0.81[AFR][1000 genomes]
rs6773521	0.81[AFR][1000 genomes]
rs6777145	0.83[AFR][1000 genomes]
rs6781941	0.81[AFR][1000 genomes]
rs73075647	0.88[EUR][1000 genomes]
rs73079603	0.94[EUR][1000 genomes]
rs7433300	0.87[AFR][1000 genomes]
rs7620997	0.84[AFR][1000 genomes]
rs9311403	0.82[AFR][1000 genomes]
rs9844122	0.85[AFR][1000 genomes]
rs9845728	0.88[AFR][1000 genomes]
rs9854790	0.88[AFR][1000 genomes]
rs9858443	0.85[AFR][1000 genomes]
rs9875235	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47069600-47089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:47070400-47089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:47074800-47088800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
5	chr3:47078800-47101400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47079400-47088800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:47079400-47095800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47079600-47088800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
10	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:47079800-47095000	Weak transcription	HMEC	breast
12	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
13	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:47080000-47095200	Weak transcription	Fetal Brain Male	brain
15	chr3:47081000-47088800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:47081400-47089000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:47081400-47089400	Strong transcription	Fetal Thymus	thymus
18	chr3:47082400-47089400	Strong transcription	Dnd41	blood
19	chr3:47083000-47088800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:47083000-47098000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:47083000-47098000	Weak transcription	A549	lung
22	chr3:47083000-47098400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:47083000-47106400	Weak transcription	Colonic Mucosa	Colon
24	chr3:47083200-47097800	Weak transcription	Gastric	stomach
25	chr3:47083200-47098000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:47083200-47098000	Weak transcription	Ovary	ovary
27	chr3:47083200-47098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
29	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
31	chr3:47083800-47097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:47083800-47097600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:47083800-47097800	Weak transcription	Fetal Brain Female	brain
34	chr3:47083800-47098000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:47083800-47098200	Weak transcription	NHLF	lung
36	chr3:47084000-47098000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:47084200-47089200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:47084200-47093800	Weak transcription	Esophagus	oesophagus
39	chr3:47084200-47094600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:47084200-47097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:47084200-47097800	Weak transcription	Spleen	Spleen
42	chr3:47084200-47098000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:47084200-47098000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:47084200-47098200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:47084200-47098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:47084200-47098200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:47084200-47098200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:47084200-47098400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:47084200-47102800	Weak transcription	HUVEC	blood vessel
50	chr3:47084400-47088800	Weak transcription	Brain Angular Gyrus	brain

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