Variant report

Variant	rs1669
Chromosome Location	chr2:55402197-55402198
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55224254..55226682-chr2:55399758..55402693,2	K562	blood:
2	chr2:55396152..55398981-chr2:55400829..55403298,2	MCF-7	breast:
3	chr2:55396357..55398246-chr2:55402197..55406122,3	MCF-7	breast:
4	chr2:55394216..55396855-chr2:55401149..55403821,2	K562	blood:
5	chr2:55065842..55066397-chr2:55402066..55403010,2	MCF-7	breast:
6	chr2:55274212..55277423-chr2:55400698..55404492,4	K562	blood:
7	chr2:55277603..55279638-chr2:55401649..55405153,3	K562	blood:
8	chr2:55256373..55258022-chr2:55400238..55403014,2	K562	blood:
9	chr2:55241288..55243824-chr2:55401386..55404364,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200086	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10167895	1.00[ASN][1000 genomes]
rs10175803	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176835	0.89[AFR][1000 genomes]
rs10179352	0.87[AFR][1000 genomes]
rs10193886	0.90[AFR][1000 genomes]
rs10200424	0.88[AFR][1000 genomes]
rs10208867	0.86[AFR][1000 genomes]
rs13395515	0.83[AFR][1000 genomes]
rs13420684	0.83[AFR][1000 genomes]
rs13427699	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1437393	0.82[AFR][1000 genomes]
rs2118284	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545477	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67085480	1.00[ASN][1000 genomes]
rs6717482	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6720077	0.88[AFR][1000 genomes]
rs6727118	0.90[AFR][1000 genomes]
rs6727131	0.88[AFR][1000 genomes]
rs6747364	0.87[AFR][1000 genomes]
rs6757361	0.85[AFR][1000 genomes]
rs9677948	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55404000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:55395600-55422800	Weak transcription	Ovary	ovary
7	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
8	chr2:55395800-55402400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:55395800-55403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:55395800-55403000	Weak transcription	Fetal Brain Male	brain
11	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
14	chr2:55396200-55402600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:55396200-55407400	Weak transcription	HepG2	liver
16	chr2:55396400-55402600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:55397000-55402400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:55397000-55402400	Weak transcription	Brain Angular Gyrus	brain
19	chr2:55397000-55402400	Weak transcription	NHDF-Ad	bronchial
20	chr2:55397000-55410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:55397200-55402600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55397200-55402600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:55397200-55450000	Weak transcription	NH-A	brain
24	chr2:55397400-55402600	Weak transcription	NHLF	lung
25	chr2:55397400-55402600	Weak transcription	Osteobl	bone
26	chr2:55397400-55402800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:55397400-55402800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:55397400-55403000	Weak transcription	HSMM	muscle
29	chr2:55397400-55411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
31	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
35	chr2:55400600-55402200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:55400800-55406400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:55401000-55402600	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:55401000-55409000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:55401200-55402400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:55401200-55402600	Weak transcription	Fetal Kidney	kidney
41	chr2:55401200-55403000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:55401600-55419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:55401800-55403000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:55401800-55409000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:55402000-55402600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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