Variant report

Variant	rs2142939
Chromosome Location	chr6:143144366-143144367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143143766..143144689-chr6:143207796..143208632,2	MCF-7	breast:
2	chr6:143142977..143144886-chr6:143184382..143186029,2	MCF-7	breast:
3	chr6:142795312..142796264-chr6:143143811..143144602,2	MCF-7	breast:
4	chr6:143143462..143146087-chr6:143265614..143267606,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

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

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

rs_ID	r²[population]
rs1040439	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198646	0.82[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198657	0.83[JPT][hapmap]
rs2328386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493985	0.89[ASN][1000 genomes]
rs573352	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs592503	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752766	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763660	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs926372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376708	0.86[EUR][1000 genomes]
rs9376711	0.91[JPT][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143133400-143145600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:143140400-143152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:143140800-143152000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:143141200-143145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:143141400-143144600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:143141400-143145000	Enhancers	Brain Hippocampus Middle	brain
7	chr6:143141400-143145000	Enhancers	Brain Substantia Nigra	brain
8	chr6:143141400-143145400	Enhancers	Fetal Lung	lung
9	chr6:143141400-143152000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:143141600-143144600	Enhancers	Fetal Muscle Leg	muscle
11	chr6:143141600-143144800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:143141600-143144800	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:143141600-143145000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:143141600-143145000	Enhancers	Adipose Nuclei	Adipose
15	chr6:143141600-143145000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr6:143141600-143152200	Weak transcription	NH-A	brain
17	chr6:143141600-143153800	Weak transcription	HSMMtube	muscle
18	chr6:143141800-143144400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:143141800-143144400	Weak transcription	HMEC	breast
20	chr6:143141800-143144800	Enhancers	Colon Smooth Muscle	Colon
21	chr6:143141800-143145000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:143141800-143145000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:143142000-143144400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:143142000-143144400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:143142000-143144400	Enhancers	Brain Anterior Caudate	brain
26	chr6:143142000-143144400	Enhancers	Psoas Muscle	Psoas
27	chr6:143142000-143144600	Enhancers	Right Atrium	heart
28	chr6:143142000-143144800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr6:143142000-143145000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:143142000-143146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:143142000-143147800	Weak transcription	Stomach Mucosa	stomach
32	chr6:143142000-143153400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:143142200-143148000	Weak transcription	A549	lung
34	chr6:143142200-143151600	Weak transcription	Osteobl	bone
35	chr6:143142200-143153400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:143142400-143144600	Enhancers	Left Ventricle	heart
37	chr6:143142400-143144600	Enhancers	Pancreas	Pancrea
38	chr6:143142400-143145000	Enhancers	Right Ventricle	heart
39	chr6:143142400-143145800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:143142400-143145800	Weak transcription	NHEK	skin
41	chr6:143142600-143147600	Weak transcription	HUVEC	blood vessel
42	chr6:143142600-143153800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:143142600-143155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:143142800-143144400	Enhancers	Esophagus	oesophagus
45	chr6:143142800-143144600	Enhancers	Lung	lung
46	chr6:143142800-143145000	Enhancers	Brain Angular Gyrus	brain
47	chr6:143142800-143145600	Weak transcription	Fetal Intestine Large	intestine
48	chr6:143142800-143147000	Enhancers	Fetal Brain Female	brain
49	chr6:143142800-143155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:143143000-143144400	Enhancers	Cortex derived primary cultured neurospheres	brain

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