Variant report

Variant	rs6709549
Chromosome Location	chr2:54740760-54740761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54739309..54741349-chr2:54741528..54743600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17045958	1.00[ASW][hapmap];0.85[LWK][hapmap]
rs60282658	1.00[AMR][1000 genomes]
rs6728822	1.00[AMR][1000 genomes]
rs6743400	1.00[AMR][1000 genomes]
rs6743902	1.00[AMR][1000 genomes]
rs72913043	1.00[AMR][1000 genomes]
rs72915014	1.00[AMR][1000 genomes]
rs72915019	1.00[AMR][1000 genomes]
rs72915028	1.00[AMR][1000 genomes]
rs72915040	1.00[AMR][1000 genomes]
rs72915054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918739	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
5	chr2:54733600-54747000	Weak transcription	Gastric	stomach
6	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
9	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
10	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
12	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
14	chr2:54738200-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:54738200-54743800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54738200-54746400	Weak transcription	NHLF	lung
18	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
19	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:54738400-54743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:54738400-54743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:54738400-54746200	Weak transcription	A549	lung
23	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:54739000-54740800	Enhancers	Brain Anterior Caudate	brain
25	chr2:54739000-54741000	Enhancers	Adipose Nuclei	Adipose
26	chr2:54739000-54741000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:54739000-54742400	Enhancers	Fetal Lung	lung
28	chr2:54739200-54740800	Enhancers	HSMMtube	muscle
29	chr2:54739200-54741000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:54739200-54742600	Enhancers	Fetal Heart	heart
31	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:54739800-54740800	Enhancers	Colon Smooth Muscle	Colon
33	chr2:54739800-54740800	Enhancers	Fetal Thymus	thymus
34	chr2:54739800-54740800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:54739800-54740800	Enhancers	Dnd41	blood
36	chr2:54740000-54740800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:54740000-54740800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:54740000-54740800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:54740000-54740800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:54740000-54740800	Enhancers	HSMM	muscle
41	chr2:54740000-54741200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:54740000-54742600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:54740200-54740800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:54740200-54743800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:54740400-54740800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:54740400-54741600	Weak transcription	Left Ventricle	heart
47	chr2:54740400-54741800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:54740400-54742000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:54740400-54742000	Weak transcription	Ovary	ovary
50	chr2:54740400-54742200	Weak transcription	Fetal Muscle Leg	muscle

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