Variant report

Variant	rs1339040
Chromosome Location	chr6:113954911-113954912
allele	C/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	CUX1	chr6:113954765-113954986	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:113946756-113954932	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:113951154..113956306-chr6:114178159..114180970,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230943	TF binding region
ENSG00000155130	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10732719	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11153426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13212281	0.92[YRI][hapmap]
rs1339041	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383805	0.83[AMR][1000 genomes]
rs1481433	0.83[AMR][1000 genomes]
rs1538460	0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2003888	1.00[AMR][1000 genomes]
rs2127989	0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs413599	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs422286	0.84[AFR][1000 genomes]
rs4632923	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4945500	0.83[AMR][1000 genomes]
rs4945960	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4945961	0.83[AMR][1000 genomes]
rs4945962	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6911610	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6917191	1.00[AMR][1000 genomes]
rs6925360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6930982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6940419	0.83[AMR][1000 genomes]
rs922722	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9320466	0.83[AMR][1000 genomes]
rs9374409	0.83[AMR][1000 genomes]
rs9374413	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs9384877	0.86[AFR][1000 genomes]
rs9387158	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387163	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400646	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400647	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400648	0.83[AMR][1000 genomes]
rs9400655	1.00[AMR][1000 genomes]

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113943000-113956400	Weak transcription	Esophagus	oesophagus
2	chr6:113946600-113956000	Flanking Active TSS	GM12878-XiMat	blood
3	chr6:113952400-113958400	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:113952600-113957000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:113952600-113957600	Weak transcription	Gastric	stomach
6	chr6:113953200-113957800	Enhancers	Primary B cells from cord blood	blood
7	chr6:113953200-113958000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr6:113953600-113956000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr6:113953800-113955600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:113953800-113955800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:113953800-113957000	Enhancers	Fetal Intestine Small	intestine
12	chr6:113953800-113958000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:113954000-113955000	Enhancers	A549	lung
14	chr6:113954000-113955200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:113954000-113955600	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:113954000-113956000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:113954000-113956200	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:113954000-113956400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:113954000-113957000	Enhancers	Stomach Mucosa	stomach
20	chr6:113954000-113957600	Weak transcription	Liver	Liver
21	chr6:113954000-113958000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:113954000-113958200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:113954000-113958400	Enhancers	Fetal Intestine Large	intestine
24	chr6:113954000-113958400	Enhancers	NHEK	skin
25	chr6:113954000-113958600	Enhancers	HepG2	liver
26	chr6:113954000-113963800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:113954200-113955000	Enhancers	HMEC	breast
28	chr6:113954200-113955200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:113954200-113955800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:113954200-113956000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr6:113954200-113956600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:113954200-113956600	Weak transcription	HSMMtube	muscle
33	chr6:113954200-113957800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:113954200-113958000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:113954200-113965600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:113954200-113970600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:113954400-113955400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:113954400-113955400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:113954400-113955800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:113954400-113955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:113954400-113955800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:113954400-113956000	Weak transcription	Small Intestine	intestine
43	chr6:113954400-113956600	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:113954400-113956800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:113954400-113957800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:113954400-113961200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:113954400-113964000	Weak transcription	Left Ventricle	heart
48	chr6:113954400-113964400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:113954600-113955600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:113954600-113955600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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