Variant report

Variant	rs557470
Chromosome Location	chr6:44409760-44409761
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	chr6:44408746..44410322-chr6:44420941..44423520,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10807300	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1293205	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1293208	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1296018	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1952979	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273667	0.86[AMR][1000 genomes]
rs2297331	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2297333	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2894572	0.87[AMR][1000 genomes]
rs34264814	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34753552	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4143678	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711781	0.82[ASN][1000 genomes]
rs475426	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs525043	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526851	0.95[ASN][1000 genomes]
rs532492	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs545455	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs548342	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559035	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564988	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67182313	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6923521	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942323	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs864127	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9369488	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9395016	0.86[AMR][1000 genomes]
rs9395017	0.86[AMR][1000 genomes]
rs9462984	0.82[ASN][1000 genomes]
rs9462985	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9462989	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472273	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][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	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv885858	chr6:44385441-44421240	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv885859	chr6:44385441-44422466	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv517370	chr6:44385441-44422689	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1850024	chr6:44388505-44422689	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 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	chr6:44376800-44424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:44388400-44424400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:44388800-44409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:44390200-44420200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:44391800-44409800	Weak transcription	Aorta	Aorta
6	chr6:44391800-44412600	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:44392800-44411800	Weak transcription	Esophagus	oesophagus
8	chr6:44393600-44411600	Weak transcription	Right Ventricle	heart
9	chr6:44394800-44410000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
11	chr6:44397200-44409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:44397400-44409800	Weak transcription	Fetal Brain Male	brain
13	chr6:44398200-44413400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:44398200-44413400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:44398400-44409800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:44398400-44410000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:44398400-44411800	Weak transcription	Lung	lung
18	chr6:44398400-44413600	Weak transcription	Brain Angular Gyrus	brain
19	chr6:44398400-44415400	Weak transcription	Small Intestine	intestine
20	chr6:44398600-44410000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:44398600-44411600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:44398600-44419600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:44400600-44413200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:44401600-44412800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:44402000-44413400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:44402200-44413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:44402200-44414400	Weak transcription	NH-A	brain
28	chr6:44402400-44413200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:44402600-44410000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:44402600-44411600	Weak transcription	Fetal Heart	heart
31	chr6:44402600-44412000	Weak transcription	Placenta	Placenta
32	chr6:44403600-44411800	Weak transcription	Gastric	stomach
33	chr6:44403600-44411800	Weak transcription	Psoas Muscle	Psoas
34	chr6:44403600-44412600	Weak transcription	Hela-S3	cervix
35	chr6:44403800-44409800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:44403800-44411000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:44403800-44412000	Weak transcription	Pancreas	Pancrea
38	chr6:44405800-44409800	Weak transcription	HepG2	liver
39	chr6:44406000-44410200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:44406200-44411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:44406600-44409800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:44406600-44410600	Strong transcription	Liver	Liver
43	chr6:44407000-44410200	Strong transcription	Ovary	ovary
44	chr6:44407400-44410000	Weak transcription	Adipose Nuclei	Adipose
45	chr6:44407400-44412200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:44407400-44414000	Weak transcription	HSMM	muscle
47	chr6:44407600-44409800	Weak transcription	Left Ventricle	heart
48	chr6:44407600-44411600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:44407600-44413600	Weak transcription	NHEK	skin
50	chr6:44407600-44413800	Weak transcription	Rectal Mucosa Donor 31	rectum

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