Variant report

Variant	rs6549210
Chromosome Location	chr3:69418057-69418058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69416233..69418620-chr3:69433830..69435946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12107294	1.00[EUR][1000 genomes]
rs13323929	1.00[EUR][1000 genomes]
rs1384932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005573	1.00[EUR][1000 genomes]
rs17005591	1.00[EUR][1000 genomes]
rs59851645	1.00[EUR][1000 genomes]
rs6549212	1.00[EUR][1000 genomes]
rs72934847	1.00[EUR][1000 genomes]
rs72934854	1.00[EUR][1000 genomes]
rs72934855	1.00[EUR][1000 genomes]
rs72934857	1.00[EUR][1000 genomes]
rs72940786	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7633864	1.00[EUR][1000 genomes]
rs7639924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9830380	1.00[EUR][1000 genomes]
rs9849228	1.00[EUR][1000 genomes]
rs9861534	1.00[EUR][1000 genomes]
rs9868554	1.00[EUR][1000 genomes]
rs9878971	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:69413600-69419000	Weak transcription	NHDF-Ad	bronchial
3	chr3:69413800-69419000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:69413800-69419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:69414000-69418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:69414000-69419000	Weak transcription	Osteobl	bone
7	chr3:69415000-69418800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:69416000-69419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:69416000-69419200	Weak transcription	Fetal Brain Male	brain
10	chr3:69416600-69418400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:69416600-69420400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:69416800-69419800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:69416800-69420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:69416800-69420600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:69417000-69419000	Enhancers	HUVEC	blood vessel
16	chr3:69417000-69419200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:69417000-69419400	Enhancers	Primary B cells from cord blood	blood
18	chr3:69417000-69420600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:69417000-69420600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:69417200-69418200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:69417200-69418200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:69417200-69418400	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:69417200-69418400	Enhancers	Fetal Thymus	thymus
24	chr3:69417200-69419000	Enhancers	HMEC	breast
25	chr3:69417200-69419000	Enhancers	NHEK	skin
26	chr3:69417200-69419400	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:69417200-69419400	Enhancers	Brain Hippocampus Middle	brain
28	chr3:69417200-69419400	Enhancers	HSMM	muscle
29	chr3:69417200-69420600	Flanking Active TSS	Dnd41	blood
30	chr3:69417200-69421000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:69417400-69418200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:69417400-69419200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:69417400-69419200	Enhancers	Brain Substantia Nigra	brain
34	chr3:69417400-69419400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:69417400-69420800	Enhancers	Fetal Lung	lung
36	chr3:69417600-69419200	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:69417600-69419400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:69417800-69418800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:69417800-69419000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:69417800-69419000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:69417800-69419000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:69417800-69419000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:69417800-69419200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:69417800-69419200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:69417800-69419200	Enhancers	Primary T cells from cord blood	blood
46	chr3:69417800-69419200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:69417800-69419200	Weak transcription	Brain Anterior Caudate	brain
48	chr3:69417800-69419400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:69417800-69419400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:69417800-69419400	Weak transcription	Duodenum Mucosa	Duodenum

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