Variant report

Variant	rs3088046
Chromosome Location	chr2:86726811-86726812
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	chr2:86669073..86671790-chr2:86726789..86729265,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP3-1	chr2:86726716-86727580	ENSG00000248011

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11127036	0.88[EUR][1000 genomes]
rs11127037	0.88[EUR][1000 genomes]
rs11889395	0.88[EUR][1000 genomes]
rs1465813	0.81[ASN][1000 genomes]
rs17027251	0.88[EUR][1000 genomes]
rs17027257	0.88[EUR][1000 genomes]
rs2367574	0.81[ASN][1000 genomes]
rs3755002	0.81[ASN][1000 genomes]
rs3770058	0.81[ASN][1000 genomes]
rs56300462	0.88[EUR][1000 genomes]
rs56724584	0.88[EUR][1000 genomes]
rs59305606	0.88[EUR][1000 genomes]
rs66912486	0.89[EUR][1000 genomes]
rs6725080	0.81[ASN][1000 genomes]
rs6735640	0.88[EUR][1000 genomes]
rs68049041	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598470	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
7	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
8	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
11	chr2:86720400-86727000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:86721400-86728000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr2:86722000-86727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:86722200-86727000	Strong transcription	Fetal Stomach	stomach
15	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:86723800-86727000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:86723800-86728000	Strong transcription	Colon Smooth Muscle	Colon
18	chr2:86724000-86727200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:86724000-86728000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr2:86724000-86728600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr2:86724000-86729600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr2:86724200-86727200	Strong transcription	Colonic Mucosa	Colon
23	chr2:86724200-86727400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:86724200-86727400	Strong transcription	Osteobl	bone
25	chr2:86724200-86727600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
26	chr2:86724200-86728600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:86724400-86727400	Strong transcription	Brain Angular Gyrus	brain
28	chr2:86724400-86728200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:86724400-86728400	Strong transcription	Left Ventricle	heart
30	chr2:86724400-86729000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr2:86724600-86728000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr2:86724600-86728000	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:86724600-86728200	ZNF genes & repeats	Dnd41	blood
34	chr2:86724600-86728400	Strong transcription	Rectal Smooth Muscle	rectum
35	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:86725200-86727200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:86725200-86727400	Strong transcription	Brain Hippocampus Middle	brain
38	chr2:86725200-86727400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:86725200-86729000	Strong transcription	Aorta	Aorta
40	chr2:86725200-86730000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:86725400-86727400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:86725400-86727600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
43	chr2:86725400-86727600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr2:86725400-86727600	Strong transcription	HSMMtube	muscle
45	chr2:86725400-86730000	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:86725600-86727200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr2:86725600-86727400	Strong transcription	Fetal Heart	heart
49	chr2:86725600-86727600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:86725600-86727800	Strong transcription	Placenta Amnion	Placenta Amnion

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