Variant report

Variant	rs1040439
Chromosome Location	chr6:143147414-143147415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143145676..143148606-chr6:143158405..143160866,2	K562	blood:
2	chr6:143146184..143148746-chr6:143152245..143154494,2	MCF-7	breast:
3	chr6:143144618..143147741-chr6:143149316..143151802,4	MCF-7	breast:
4	chr6:143146689..143151970-chr6:143152746..143156314,7	MCF-7	breast:
5	chr6:143016859..143019440-chr6:143145754..143147934,2	K562	blood:
6	chr6:143139378..143142104-chr6:143146552..143148594,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs198646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198653	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs198657	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2142939	0.80[CEU][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2328386	0.80[CEU][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2328387	0.80[CEU][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493985	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592503	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752766	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7763660	0.83[ASN][1000 genomes]
rs926372	0.80[CEU][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376711	0.86[CEU][hapmap];0.90[CHB][hapmap]

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	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1019558	chr6:143121577-143154554	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143140400-143152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:143140800-143152000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:143141400-143152000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:143141600-143152200	Weak transcription	NH-A	brain
5	chr6:143141600-143153800	Weak transcription	HSMMtube	muscle
6	chr6:143142000-143147800	Weak transcription	Stomach Mucosa	stomach
7	chr6:143142000-143153400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:143142200-143148000	Weak transcription	A549	lung
9	chr6:143142200-143151600	Weak transcription	Osteobl	bone
10	chr6:143142200-143153400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:143142600-143147600	Weak transcription	HUVEC	blood vessel
12	chr6:143142600-143153800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:143142600-143155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:143142800-143155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:143143200-143153800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:143143400-143147600	Weak transcription	Fetal Heart	heart
17	chr6:143143400-143148600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:143143400-143152000	Weak transcription	Gastric	stomach
19	chr6:143143400-143157400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:143143400-143159600	Weak transcription	HepG2	liver
21	chr6:143143400-143160600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:143143800-143151400	Weak transcription	Thymus	Thymus
23	chr6:143144000-143151800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:143144000-143152000	Weak transcription	Primary B cells from cord blood	blood
25	chr6:143144000-143153800	Weak transcription	HSMM	muscle
26	chr6:143144000-143165800	Weak transcription	Liver	Liver
27	chr6:143144200-143154200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:143144200-143156000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr6:143144600-143152000	Weak transcription	Pancreas	Pancrea
30	chr6:143144600-143163000	Weak transcription	Dnd41	blood
31	chr6:143144600-143163200	Weak transcription	Fetal Thymus	thymus
32	chr6:143144800-143147800	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:143144800-143148600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:143144800-143148600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:143144800-143148600	Weak transcription	HMEC	breast
36	chr6:143144800-143162400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:143144800-143163000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:143144800-143166800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:143145000-143150600	Weak transcription	GM12878-XiMat	blood
40	chr6:143145400-143149400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:143145800-143148400	Weak transcription	Placenta	Placenta
42	chr6:143146000-143150800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:143146000-143151400	Weak transcription	Brain Substantia Nigra	brain
44	chr6:143146000-143151800	Weak transcription	Lung	lung
45	chr6:143146000-143152000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:143146000-143153600	Weak transcription	NHLF	lung
47	chr6:143146000-143154000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:143146000-143154200	Weak transcription	Brain Anterior Caudate	brain
49	chr6:143146000-143156200	Weak transcription	Brain Angular Gyrus	brain
50	chr6:143146200-143148400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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