Variant report

Variant	rs1550241
Chromosome Location	chr2:190540164-190540165
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	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128694	Chromatin interaction
ENSG00000253559	Chromatin interaction

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

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

rs_ID	r²[population]
rs1020151	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10209441	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10931429	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11888722	1.00[AMR][1000 genomes]
rs1225086	1.00[AMR][1000 genomes]
rs1225103	1.00[AMR][1000 genomes]
rs12693550	1.00[ASW][hapmap];0.88[LWK][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs1437880	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1550242	1.00[AMR][1000 genomes]
rs2019099	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2118454	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2254040	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs2263968	1.00[AMR][1000 genomes]
rs2352288	1.00[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs5742992	1.00[AMR][1000 genomes]
rs5742999	1.00[AMR][1000 genomes]
rs5743205	1.00[AMR][1000 genomes]
rs6723158	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893783	0.88[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs930426	1.00[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190530000-190542800	Strong transcription	Dnd41	blood
3	chr2:190534000-190550200	Weak transcription	K562	blood
4	chr2:190538600-190540200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr2:190538600-190540200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:190538600-190540200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr2:190538600-190540200	Flanking Active TSS	HUVEC	blood vessel
8	chr2:190538600-190540400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:190538600-190540400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:190538800-190540200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:190538800-190540200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:190538800-190540200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr2:190538800-190540200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:190538800-190540200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr2:190538800-190540200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr2:190538800-190540200	Active TSS	Psoas Muscle	Psoas
17	chr2:190538800-190540200	Active TSS	Right Atrium	heart
18	chr2:190538800-190540400	Active TSS	NHDF-Ad	bronchial
19	chr2:190539000-190540200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr2:190539000-190540200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:190539000-190540200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr2:190539000-190540200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:190539000-190540200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:190539000-190540200	Active TSS	Brain Cingulate Gyrus	brain
25	chr2:190539000-190540200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:190539000-190540200	Active TSS	Colon Smooth Muscle	Colon
27	chr2:190539000-190540200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:190539000-190540200	Active TSS	Fetal Brain Female	brain
29	chr2:190539000-190540200	Active TSS	Fetal Stomach	stomach
30	chr2:190539000-190540200	Active TSS	Right Ventricle	heart
31	chr2:190539000-190540400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:190539000-190540400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:190539000-190540400	Active TSS	A549	lung
34	chr2:190539000-190540400	Active TSS	NHLF	lung
35	chr2:190539200-190540200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:190539200-190540200	Active TSS	Duodenum Mucosa	Duodenum
37	chr2:190539200-190540200	Active TSS	Fetal Muscle Leg	muscle
38	chr2:190539200-190540200	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr2:190539200-190540400	Active TSS	HSMM	muscle
40	chr2:190539200-190540600	Active TSS	Hela-S3	cervix
41	chr2:190539400-190540200	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr2:190539400-190540200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:190539400-190540400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:190539400-190540600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr2:190539600-190540200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr2:190539600-190540200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr2:190539600-190540200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr2:190539600-190540200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr2:190539600-190540200	Flanking Active TSS	Fetal Lung	lung
50	chr2:190539600-190540200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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