Variant report

Variant	rs6549235
Chromosome Location	chr3:69590125-69590126
allele	G/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	STAT3	chr3:69590076-69590558	MCF10A-Er-Src	breast:	n/a	chr3:69590329-69590337 chr3:69590323-69590343 chr3:69590329-69590338 chr3:69590364-69590384 chr3:69590327-69590338 chr3:69590368-69590379 chr3:69590328-69590337
2	MYC	chr3:69590052-69590160	MCF10A-Er-Src	breast:	n/a	chr3:69590112-69590128
3	STAT3	chr3:69589879-69590827	MCF10A-Er-Src	breast:	n/a	chr3:69590329-69590337 chr3:69590323-69590343 chr3:69590329-69590338 chr3:69590364-69590384 chr3:69590327-69590338 chr3:69590368-69590379 chr3:69590328-69590337
4	STAT3	chr3:69589923-69590642	MCF10A-Er-Src	breast:	n/a	chr3:69590329-69590337 chr3:69590323-69590343 chr3:69590329-69590338 chr3:69590364-69590384 chr3:69590327-69590338 chr3:69590368-69590379 chr3:69590328-69590337
5	MYC	chr3:69590052-69591117	MCF10A-Er-Src	breast:	n/a	chr3:69590112-69590128 chr3:69591042-69591049

Variant related genes	Relation type
ENSG00000240265	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs55638663	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549231	1.00[CEU][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549236	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6549238	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6762368	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9310164	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9818139	0.83[ASN][1000 genomes]

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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3426797	chr3:69433086-69777229	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69588800-69590800	Active TSS	Fetal Brain Female	brain
2	chr3:69589400-69591000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:69589400-69591000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:69589600-69592400	Active TSS	HMEC	breast
5	chr3:69589800-69590200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:69589800-69590400	Flanking Active TSS	Fetal Lung	lung
7	chr3:69589800-69590800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr3:69589800-69591200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:69589800-69592400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:69589800-69592400	Active TSS	Brain Anterior Caudate	brain
11	chr3:69589800-69592400	Active TSS	Brain Substantia Nigra	brain
12	chr3:69590000-69590200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr3:69590000-69590200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:69590000-69590200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr3:69590000-69590200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr3:69590000-69590200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:69590000-69590200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:69590000-69590200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
19	chr3:69590000-69590200	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr3:69590000-69590200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
21	chr3:69590000-69590200	Active TSS	Right Atrium	heart
22	chr3:69590000-69590200	Flanking Active TSS	Right Ventricle	heart
23	chr3:69590000-69590200	Transcr. at gene 5' and 3'	NHEK	skin
24	chr3:69590000-69590400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:69590000-69590400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr3:69590000-69590400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:69590000-69590400	Enhancers	Placenta	Placenta
28	chr3:69590000-69590400	Enhancers	Pancreas	Pancrea
29	chr3:69590000-69590600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:69590000-69590600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
31	chr3:69590000-69590600	Enhancers	Fetal Heart	heart
32	chr3:69590000-69590800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr3:69590000-69590800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr3:69590000-69590800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
35	chr3:69590000-69590800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr3:69590000-69590800	Bivalent/Poised TSS	Fetal Kidney	kidney
37	chr3:69590000-69591000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:69590000-69591200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
39	chr3:69590000-69591200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr3:69590000-69591600	Active TSS	Spleen	Spleen
41	chr3:69590000-69592200	Active TSS	Brain Cingulate Gyrus	brain
42	chr3:69590000-69592200	Active TSS	Brain Hippocampus Middle	brain
43	chr3:69590000-69592400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:69590000-69592400	Active TSS	Brain Angular Gyrus	brain
45	chr3:69590000-69592600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:69590000-69592600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr3:69590000-69592600	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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