Variant report

Variant	rs3820
Chromosome Location	chr2:86729549-86729550
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP3-1	chr2:86727619-86729774	ENSG00000248011

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12464501	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468191	0.81[ASN][1000 genomes]
rs12471953	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2044231	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2044232	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55708554	0.81[EUR][1000 genomes]
rs68049041	0.95[ASN][1000 genomes]
rs73946206	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:86724000-86729600	ZNF genes & repeats	GM12878-XiMat	blood
6	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr2:86725200-86730000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:86725400-86730000	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:86726000-86729600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
11	chr2:86726000-86729600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:86726000-86729800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr2:86726000-86731200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:86726200-86729800	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr2:86726200-86729800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr2:86726400-86735400	Weak transcription	NHLF	lung
17	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
18	chr2:86726400-86741800	Weak transcription	NH-A	brain
19	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
21	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
22	chr2:86726800-86739000	Weak transcription	K562	blood
23	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:86727400-86731000	Weak transcription	Osteobl	bone
25	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
26	chr2:86727600-86731800	Weak transcription	HSMMtube	muscle
27	chr2:86727600-86732600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:86727600-86734600	Weak transcription	HMEC	breast
29	chr2:86727800-86732000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:86728000-86729600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:86728000-86729600	Weak transcription	Fetal Thymus	thymus
32	chr2:86728000-86729600	Weak transcription	Small Intestine	intestine
33	chr2:86728000-86729800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:86728000-86730400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:86728000-86730600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:86728000-86730600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:86728000-86731000	Weak transcription	Esophagus	oesophagus
38	chr2:86728000-86731000	Weak transcription	Pancreas	Pancrea
39	chr2:86728000-86731800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:86728000-86731800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:86728000-86732000	Weak transcription	Brain Angular Gyrus	brain
42	chr2:86728000-86732000	Weak transcription	Fetal Kidney	kidney
43	chr2:86728000-86732000	Weak transcription	Gastric	stomach
44	chr2:86728000-86732400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:86728000-86732600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:86728000-86734200	Weak transcription	HSMM	muscle
47	chr2:86728000-86737600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:86728000-86737600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:86728000-86737600	Strong transcription	Adipose Nuclei	Adipose
50	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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