Variant report

Variant	rs60620079
Chromosome Location	chr6:56509977-56509978
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56508417..56510652-chr6:56534846..56537017,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1323321	1.00[AMR][1000 genomes]
rs4413617	1.00[AMR][1000 genomes]
rs4520018	1.00[AMR][1000 genomes]
rs57183853	1.00[AMR][1000 genomes]
rs57439200	1.00[AMR][1000 genomes]
rs57936670	1.00[AMR][1000 genomes]
rs58912662	1.00[AMR][1000 genomes]
rs59493539	1.00[AMR][1000 genomes]
rs59801210	1.00[AMR][1000 genomes]
rs60143048	1.00[AMR][1000 genomes]
rs60172134	1.00[AMR][1000 genomes]
rs60304191	1.00[AMR][1000 genomes]
rs7748364	0.97[AFR][1000 genomes]
rs7753074	1.00[AMR][1000 genomes]
rs7760701	0.82[AFR][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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
2	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
3	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
4	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
7	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
8	chr6:56478400-56514600	Weak transcription	Lung	lung
9	chr6:56480600-56514600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:56480800-56536400	Weak transcription	Gastric	stomach
11	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:56483400-56512600	Weak transcription	Psoas Muscle	Psoas
13	chr6:56485000-56514400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:56485800-56512400	Weak transcription	Fetal Stomach	stomach
15	chr6:56490000-56513600	Strong transcription	Fetal Intestine Large	intestine
16	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
17	chr6:56496600-56517000	Weak transcription	Fetal Brain Male	brain
18	chr6:56496800-56515000	Weak transcription	Fetal Kidney	kidney
19	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:56499400-56510000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:56499400-56511800	Weak transcription	Ovary	ovary
22	chr6:56499400-56516800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:56500600-56514200	Weak transcription	Fetal Heart	heart
24	chr6:56500800-56513000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:56502000-56512400	Weak transcription	Fetal Intestine Small	intestine
27	chr6:56505400-56510000	Weak transcription	Placenta	Placenta
28	chr6:56505400-56514600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:56505600-56510000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:56505600-56510000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:56505600-56511800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:56505600-56522000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:56505600-56537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:56505800-56510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:56506000-56516000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:56507200-56511000	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:56507400-56515800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:56507800-56514400	Weak transcription	Aorta	Aorta
39	chr6:56508200-56510000	Weak transcription	Brain Substantia Nigra	brain
40	chr6:56508200-56514000	Weak transcription	Hela-S3	cervix
41	chr6:56508200-56514600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:56508200-56520000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:56508400-56510000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:56508400-56510000	Weak transcription	HepG2	liver
45	chr6:56508400-56512000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:56508600-56510400	Enhancers	NHEK	skin
47	chr6:56508800-56511800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:56508800-56513800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:56508800-56514200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:56508800-56514600	Strong transcription	HSMMtube	muscle

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