Variant report

Variant	rs28633631
Chromosome Location	chr6:56520960-56520961
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56517201..56519580-chr6:56519629..56522798,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1024196	1.00[EUR][1000 genomes]
rs11963288	0.94[EUR][1000 genomes]
rs11966986	1.00[EUR][1000 genomes]
rs11967796	1.00[EUR][1000 genomes]
rs11970410	1.00[EUR][1000 genomes]
rs1407831	0.89[EUR][1000 genomes]
rs1535609	0.94[EUR][1000 genomes]
rs1535611	0.94[EUR][1000 genomes]
rs16887928	0.89[EUR][1000 genomes]
rs16888070	1.00[EUR][1000 genomes]
rs16888106	1.00[EUR][1000 genomes]
rs2144407	1.00[EUR][1000 genomes]
rs2180148	1.00[EUR][1000 genomes]
rs2207678	1.00[EUR][1000 genomes]
rs2397224	0.89[EUR][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.94[EUR][1000 genomes]
rs41267673	1.00[EUR][1000 genomes]
rs41271848	0.89[EUR][1000 genomes]
rs41271850	0.89[EUR][1000 genomes]
rs41271854	0.94[EUR][1000 genomes]
rs41271856	0.94[EUR][1000 genomes]
rs41271872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41271876	1.00[EUR][1000 genomes]
rs41271878	1.00[EUR][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4288197	0.84[EUR][1000 genomes]
rs45442999	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45553042	0.95[EUR][1000 genomes]
rs56991168	0.81[EUR][1000 genomes]
rs57289287	1.00[EUR][1000 genomes]
rs57350484	1.00[EUR][1000 genomes]
rs57790896	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57822928	0.94[EUR][1000 genomes]
rs58487319	0.81[EUR][1000 genomes]
rs58565063	1.00[EUR][1000 genomes]
rs58730144	0.94[EUR][1000 genomes]
rs59772940	1.00[EUR][1000 genomes]
rs59864125	0.94[EUR][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	1.00[EUR][1000 genomes]
rs6459168	1.00[EUR][1000 genomes]
rs6900572	1.00[EUR][1000 genomes]
rs6903517	0.85[EUR][1000 genomes]
rs6903815	1.00[EUR][1000 genomes]
rs6941626	1.00[EUR][1000 genomes]
rs73455767	0.94[EUR][1000 genomes]
rs73455782	0.94[EUR][1000 genomes]
rs73455797	0.81[EUR][1000 genomes]
rs73465854	0.94[EUR][1000 genomes]
rs73746926	1.00[EUR][1000 genomes]
rs73746929	1.00[EUR][1000 genomes]
rs73747826	0.89[EUR][1000 genomes]
rs73747832	0.89[EUR][1000 genomes]
rs73749935	0.94[EUR][1000 genomes]
rs73749942	0.94[EUR][1000 genomes]
rs73749948	0.94[EUR][1000 genomes]
rs73749949	0.94[EUR][1000 genomes]
rs7749100	1.00[EUR][1000 genomes]
rs7759479	1.00[EUR][1000 genomes]
rs7760503	1.00[EUR][1000 genomes]
rs7760515	1.00[EUR][1000 genomes]
rs7760542	1.00[EUR][1000 genomes]
rs7760701	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761027	1.00[EUR][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
2	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
3	chr6:56480800-56536400	Weak transcription	Gastric	stomach
4	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
5	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:56505600-56522000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:56505600-56537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:56509800-56528200	Weak transcription	Esophagus	oesophagus
10	chr6:56511600-56524600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:56512400-56524600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:56512600-56534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:56513000-56534400	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:56513200-56524400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:56514200-56521200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:56514800-56537000	Weak transcription	Lung	lung
17	chr6:56515000-56521000	Weak transcription	Liver	Liver
18	chr6:56515000-56524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:56515000-56524600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:56515000-56534400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:56515800-56524400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:56516600-56524800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:56517400-56524400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:56517400-56524600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:56517400-56536400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:56518200-56521000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:56518200-56521800	Enhancers	A549	lung
28	chr6:56518200-56522400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:56518200-56522400	Weak transcription	HSMMtube	muscle
30	chr6:56518200-56524600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:56518200-56524600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:56518200-56524600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:56518200-56524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:56518600-56524600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:56518600-56524600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:56518800-56521000	Weak transcription	Small Intestine	intestine
37	chr6:56519000-56521000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:56519000-56523200	Weak transcription	GM12878-XiMat	blood
39	chr6:56519000-56524600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:56519000-56524800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:56519000-56524800	Weak transcription	NH-A	brain
42	chr6:56519200-56523000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:56519600-56521200	Enhancers	Ovary	ovary
44	chr6:56519800-56521000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:56519800-56521400	Enhancers	Fetal Lung	lung
46	chr6:56519800-56522000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:56519800-56523000	Enhancers	Primary hematopoietic stem cells	blood
48	chr6:56520000-56521200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:56520000-56521400	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:56520000-56521400	Enhancers	K562	blood

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